ALBERT

Description: A novel three-dimensional (3D) CdII coordination polymer, namely, poly[[μ2-4,4′-bis(2-methylimidazol-1-yl)-[1,1′-biphenyl]](μ2-5-methylisophthalato)cadmium(II)], [Cd(C9H6O4)(C20H18N4)] n or [Cd(MIP)(4,4′-BMIBP)] n , (I), was synthesized by the hydrothermal method using 5-methylisophthalic acid (H2MIP), 4,4′-bis(2-methylimidazol-1-yl)-[1,1′-biphenyl] (4,4′-BMIBP) and Cd(NO3)2·6H2O, and characterized by single-crystal X-ray diffraction, elemental analysis, IR spectroscopy and thermogravimetric analysis. Compound (I) exhibits a novel fivefold interpenetrating 3D diamondoid framework. Additionally, it shows fluorescence emission in the solid state and promising photocatalytic activities for the degradation of methylene blue (MB) in water at room temperature.

Description: The study of various forms of pharmaceutical substances with specific physicochemical properties suitable for putting them on the market is one of the elements of research in the pharmaceutical industry. A large proportion of active pharmaceutical ingredients (APIs) occur in the salt form. The use of an acidic coformer with a given structure and a suitable pK a value towards purine alkaloids containing a basic imidazole N atom can lead to salt formation. In this work, 2,6-dihydroxybenzoic acid (26DHBA) was used for cocrystallization of theobromine (TBR) and caffeine (CAF). Two novel salts, namely, theobrominium 2,6-dihydroxybenzoate, C7H9N4O2 +·C7H5O4 − (I), and caffeinium 2,6-dihydroxybenzoate, C8H11N4O2 +·C7H5O4 − (II), were synthesized. Both salts were obtained independently by slow evaporation from solution, by neat grinding and also by microwave-assisted slurry cocrystallization. Powder X-ray diffraction measurements proved the formation of the new substances. Single-crystal X-ray diffraction studies confirmed proton transfer between the given alkaloid and 26DHBA, and the formation of N—H...O hydrogen bonds in both I and II. Unlike the caffeine cations in II, the theobromine cations in I are paired by noncovalent N—H...O=C interactions and a cyclic array is observed. As expected, the two hydroxy groups in the 26DHBA anion in both salts are involved in two intramolecular O—H...O hydrogen bonds. C—H...O and π–π interactions further stabilize the crystal structures of both compounds. Steady-state UV–Vis spectroscopy showed changes in the water solubility of xanthines after ionizable complex formation. The obtained salts I and II were also characterized by theoretical calculations, Fourier-transform IR spectroscopy (FT–IR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and elemental analysis.

Description: β-Mannanase (EC 3.2.1.78) is an enzyme that cleaves within the backbone of mannan-based polysaccharides at β-1,4-linked D-mannose residues, resulting in the formation of mannooligosaccharides (MOS), which are potential prebiotics. The GH26 β-mannanase KMAN from Klebsiella oxytoca KUB-CW2-3 shares 49–72% amino-acid sequence similarity with β-mannanases from other sources. The crystal structure of KMAN at a resolution of 2.57 Å revealed an open cleft-shaped active site. The enzyme structure is based on a (β/α)8-barrel architecture, which is a typical characteristic of clan A glycoside hydrolase enzymes. The putative catalytic residues Glu183 and Glu282 are located on the loop connected to β-strand 4 and at the end of β-strand 7, respectively. KMAN digests linear MOS with a degree of polymerization (DP) of between 4 and 6, with high catalytic efficiency (k cat/K m) towards DP6 (2571.26 min−1 mM −1). The predominant end products from the hydrolysis of locust bean gum, konjac glucomannan and linear MOS are mannobiose and mannotriose. It was observed that KMAN requires at least four binding sites for the binding of substrate molecules and hydrolysis. Molecular docking of mannotriose and galactosyl-mannotetraose to KMAN confirmed its mode of action, which prefers linear substrates to branched substrates.

Description: Hepatitis C virus (HCV) is an enveloped RNA virus. One of the hallmarks of HCV infection is a rearrangement of the host cell membranes, known as the `membranous web'. Full-field cryo soft X-ray tomography (cryo-SXT) in the water-window energy range (284–543 eV) was performed on the MISTRAL beamline to investigate, in whole unstained cells, the morphology of the membranous rearrangements induced in HCV replicon-harbouring cells in conditions close to the living physiological state. All morphological alterations could be reverted by a combination of sofosbuvir/daclatasvir, which are clinically approved antivirals (direct-acting antivirals; DAAs) for HCV infection. Correlatively combining cryo-SXT and 2D synchrotron-based infrared microscopy provides critical information on the chemical nature of specific infection-related structures, which allows specific patterns of the infection process or the DAA-mediated healing process to be distinguished.

Description: The initiation of infection of host tissues by Staphylococcus aureus requires a family of staphylococcal adhesive proteins containing serine–aspartate repeat (SDR) domains, such as ClfA. The O-linked glycosylation of the long-chain SDR domain mediated by SdgB and SdgA is a key virulence factor that protects the adhesive SDR proteins against host proteolytic attack in order to promote successful tissue colonization, and has also been implicated in staphylococcal agglutination, which leads to sepsis and an immunodominant epitope for a strong antibody response. Despite the biological significance of these two glycosyltransferases involved in pathogenicity and avoidance of the host innate immune response, their structures and the molecular basis of their activity have not been investigated. This study reports the crystal structures of SdgB and SdgA from S. aureus as well as multiple structures of SdgB in complex with its substrates (for example UDP, N-acetylglucosamine or SDR peptides), products (glycosylated SDR peptides) or phosphate ions. Together with biophysical and biochemical analyses, this structural work uncovered the novel mechanism by which SdgB and SdgA carry out the glycosyl-transfer process to the long SDR region in SDR proteins. SdgB undergoes dynamic changes in its structure such as a transition from an open to a closed conformation upon ligand binding and takes diverse forms, both as a homodimer and as a heterodimer with SdgA. Overall, these findings not only elucidate the putative role of the three domains of SdgB in recognizing donor and acceptor substrates, but also provide new mechanistic insights into glycosylation of the SDR domain, which can serve as a starting point for the development of antibacterial drugs against staphylococcal infections.

Description: The acetylxylan esterases (AXEs) classified into carbohydrate esterase family 4 (CE4) are metalloenzymes that catalyze the deacetylation of acetylated carbohydrates. AXE from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866), which belongs to CE4, is composed of three parts: a signal sequence (residues 1–22), an N-terminal region (NTR; residues 23–135) and a catalytic domain (residues 136–324). TTE0866 catalyzes the deacetylation of highly substituted cellulose acetate and is expected to be useful for industrial applications in the reuse of resources. In this study, the crystal structure of TTE0866 (residues 23–324) was successfully determined. The crystal diffracted to 1.9 Å resolution and belonged to space group I212121. The catalytic domain (residues 136–321) exhibited a (β/α)7-barrel topology. However, electron density was not observed for the NTR (residues 23–135). The crystal packing revealed the presence of an intermolecular space without observable electron density, indicating that the NTR occupies this space without a defined conformation or was truncated during the crystallization process. Although the active-site conformation of TTE0866 was found to be highly similar to those of other CE4 enzymes, the orientation of its Trp264 side chain near the active site was clearly distinct. The unique orientation of the Trp264 side chain formed a different-shaped cavity within TTE0866, which may contribute to its reactivity towards highly substituted cellulose acetate.

Description: The design and synthesis of metal–organic frameworks (MOFs) have attracted much interest due to the aesthetics of their crystalline architectures and their potential applications as new functional materials. A new twofold interpenetrated three-dimensional (3D) MOF, namely, poly[[triaqua(μ4-(2R,2′R)-2,2′-{[1,4-phenylenebis(carbonyl)]bis(azanediyl)}dipropionato-κ7 O 1:O 1,O 1′:O 4:O 4,O 4′,O 4′′)(μ3-(2R,2′R)-2,2′-{[1,4-phenylenebis(carbonyl)]bis(azanediyl)}dipropionato-κ3 O 1:O 4:O 4)dicadmium(II)] dihydrate], {[Cd2(C14H14N2O6)2(H2O)3]·2H2O} n , (I), has been synthesized by the reaction of Cd(CH3COO)2·2H2O with the synthesized ligand (2R,2′R)-2,2′-{[1,4-phenylenebis(carbonyl)]bis(azanediyl)}dipropionic acid (H2 L). Single-crystal X-ray diffraction analysis reveals that the carboxylate groups from two crystallographically independent L 2− dianions link the cadmium cations into a one-dimensional helical secondary building unit (SBU). The resulting SBUs are extended into a 3D metal–organic framework via the terephthalamide moiety of the ligand as a spacer. In the crystal, two independent MOFs interpenetrate each other, thus producing a twofold interpenetrated 3D architecture, which shows an unprecedented 2-nodal (7,9)-connected net with the point (Schläfli) symbol (37·46·58)(38·411·516·6). MOF (I) was further characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction and thermogravimetric analysis. The photoluminescence properties and UV–Vis absorption spectrum of (I) have also been investigated. The MOF exhibits enhanced fluorescence emission with a high photoluminescence quantum yield of 31.55% and a longer lifetime compared with free H2 L.

Description: In crystallography, the phase problem can often be addressed by the careful preparation of molecular-replacement search models. This has led to the development of pipelines such as MrBUMP that can automatically identify homologous proteins from an input sequence and edit them to focus on the areas that are most conserved. Many of these approaches can be applied directly to cryo-EM to help discover, prepare and correctly place models (here called cryo-EM search models) into electrostatic potential maps. This can significantly reduce the amount of manual model building that is required for structure determination. Here, MrBUMP is repurposed to fit automatically obtained PDB-derived chains and domains into cryo-EM maps. MrBUMP was successfully able to identify and place cryo-EM search models across a range of resolutions. Methods such as map segmentation are also explored as potential routes to improved performance. Map segmentation was also found to improve the effectiveness of the pipeline for higher resolution (

Description: We present a series of experiments to explore the dynamics of particle-laden fountains rising through a stratified environment with zero buoyancy flux at the source. We find that the ratio $U$ between the particle sedimentation speed $V_s$ and the characteristic fountain velocity $(M_0N^{2})^{1/4}$ , where $M_0$ is the initial momentum flux and $N$ the frequency of the ambient stratification, has a profound effect on the structure of the fountain and the dispersal of the particles. In a mono-disperse particle fountain, when the settling speed of the particles is small in comparison to the characteristic fountain speed ( $Ull 1$ ) the flow initially behaves in an analogous fashion to a single-phase fountain, forming an intrusion at a height of approximately 0.5 of the maximum fountain height. As the fluid–particle mixture spreads out, the particles gradually sediment to the tank floor. The intruding fluid subsequently rises and forms a new intrusion at its neutral buoyancy height. Some of the particles are carried up from the original intrusion with the rising fluid. This leads to the formation of a sedimenting column of particles with a characteristic radius. We observe a transition in the behaviour of the particle fountains in the vicinity of $Usim 0.1$ , with the particles now separating from the fluid near the top of the fountain. The separation of the particles leads to a reduction in the steady-state height of the particle-laden fountain, while the fluid in the fountain continues upwards until reaching its neutral buoyancy height and forming an intrusion above the fountain top. We compare the experimental data with two models of turbulent fountains to help rationalise the trends observed as a function of the dimensionless fall speed $U$ . We briefly consider the dynamics of poly-disperse particle fountains and relate their dynamics to the regimes observed in their mono-disperse counterparts. We discuss the implications of this work for the dispersal of different sized particles from submarine volcanic eruptions.

Description: Ensemble refinement, the application of molecular dynamics to crystallographic refinement, explicitly models the disorder inherent in macromolecular structures. These ensemble models have been shown to produce more accurate structures than traditional single-model structures. However, suboptimal sampling of the molecular-dynamics simulation and modelling of crystallographic disorder has limited the utility of the method, and can lead to unphysical and strained models. Here, two improvements to the ensemble refinement method implemented within Phenix are presented: DEN restraints, which guide the local sampling of conformations and allow a more robust exploration of local conformational landscapes, and ECHT disorder models, which allow the selection of more physically meaningful and effective disorder models for parameterizing the continuous disorder components within a crystal. These improvements lead to more consistent and physically interpretable simulations of macromolecules in crystals, and allow structural heterogeneity and disorder to be systematically explored on different scales. The new approach is demonstrated on several case studies and the SARS-CoV-2 main protease, and demonstrates how the choice of disorder model affects the type of disorder that is sampled by the restrained molecular-dynamics simulation.

Description: The structure determinations of phases (II) and (III) of barium dicalcium hexakis(propanoate) {or poly[hexa-μ4-propanoato-bariumdicalcium], [BaCa2(C3H5O2)6] n } are reported at 240 and 130 K, respectively [phase (I) was determined previously by Stadnicka & Glazer (1980). Acta Cryst. B36, 2977–2985; our structure determination of phase (I) at room temperature is included in the supporting information]. In the high-temperature phase, the Ba2+ cation is surrounded by six carboxylate groups in bidentate bridging modes. In the low-temperature phases, five carboxylate groups act in bidentate bridging modes and one acts in a monodentate bridging mode around Ba2+. The Ca2+ cations are surrounded by six carboxylate O atoms in a trigonal antiprism in all the structures. The Ba2+ and Ca2+ cations are underbonded and significantly overbonded, respectively, in all the phases. The bonding of the Ba2+ cation increases slightly at the cost of the bonding of Ca2+ cations during cooling to the low-temperature phases. The phase transitions during cooling are accompanied by ordering of the ethyl chains. In room-temperature phase (I), all six ethyl chains are positionally disordered over two positions in the crossed mode, with additional splitting of the ethyl α- and β-C atoms. In phase (II), on the other hand, there are three disordered ethyl chains, one with positionally disordered ethyl α- and β-C atoms, and the other two with positionally disordered ethyl β-C atoms only, and in the lowest-temperature phase (III) there are four ordered ethyl chains and two disordered ethyl chains with positionally disordered ethyl β-C atoms only.

Description: Azotobacter vinelandii is a model diazotroph and is the source of most nitrogenase material for structural and biochemical work. Azotobacter can grow in above-atmospheric levels of oxygen, despite the sensitivity of nitrogenase activity to oxygen. Azotobacter has many iron–sulfur proteins in its genome, which were identified as far back as the 1960s and probably play roles in the complex redox chemistry that Azotobacter must maintain when fixing nitrogen. Here, the 2.1 Å resolution crystal structure of the [2Fe–2S] protein I (Shethna protein I) from A. vinelandii is presented, revealing a homodimer with the [2Fe–2S] cluster coordinated by the surrounding conserved cysteine residues. It is similar to the structure of the thioredoxin-like [2Fe–2S] protein from Aquifex aeolicus, including the positions of the [2Fe–2S] clusters and conserved cysteine residues. The structure of Shethna protein I will provide information for understanding its function in relation to nitrogen fixation and its evolutionary relationships to other ferredoxins.

Description: The multislice method, which simulates the propagation of the incident electron wavefunction through a crystal, is a well established method for analysing the multiple scattering effects that an electron beam may undergo. The inclusion of magnetic effects into this method proves crucial towards simulating enhanced magnetic interaction of vortex beams with magnetic materials, calculating magnetic Bragg spots or searching for magnon signatures, to name a few examples. Inclusion of magnetism poses novel challenges to the efficiency of the multislice method for larger systems, especially regarding the consistent computation of magnetic vector potentials A and magnetic fields B over large supercells. This work presents a tabulation of parameterized magnetic (PM) values for the first three rows of transition metal elements computed from atomic density functional theory (DFT) calculations, allowing for the efficient computation of approximate A and B across large crystals using only structural and magnetic moment size and direction information. Ferromagnetic b.c.c. (body-centred cubic) Fe and tetragonal FePt are chosen to showcase the performance of PM values versus directly obtaining A and B from the unit-cell spin density by DFT. The magnetic fields of b.c.c. Fe are well described by the PM approach while for FePt the PM approach is less accurate due to deformations in the spin density. Calculations of the magnetic signal, namely the change due to A and B of the intensity of diffraction patterns, show that the PM approach for both b.c.c. Fe and FePt is able to describe the effects of magnetism in these systems to a good degree of accuracy.

Description: Glutamine synthetase (GS) is a decameric enzyme that plays a key role in nitrogen metabolism. Acetylation of the N-terminal degron (N-degron) of GS is essential for ubiquitylation and subsequent GS degradation. The full-length GS structure showed that the N-degron is buried inside the GS decamer and is inaccessible to the acetyltransferase. The structure of N-degron-truncated GS reported here reveals that the N-degron is not essential for GS decamer formation. It is also shown that the N-degron can be exposed to a solvent region through a series of conformational adjustments upon ligand binding. In summary, this study elucidated the dynamic movement of the N-degron and the possible effect of glutamine in enhancing the acetylation process.

Description: The predictive power of simulation has become embedded in the infrastructure of modern economies. Computer-aided design is ubiquitous throughout industry. In aeronautical engineering, built infrastructure and materials manufacturing, simulations are routinely used to compute the performance of potential designs before construction. The ability to predict the behaviour of products is a driver of innovation by reducing the cost barrier to new designs, but also because radically novel ideas can be piloted with relatively little risk. Accurate weather forecasting is essential to guide domestic and military flight paths, and therefore the underpinning simulations are critical enough to have implications for national security. However, in the pharmaceutical and biotechnological industries, the application of computer simulations remains limited by the capabilities of the technology with respect to the complexity of molecular biology and human physiology. Over the last 30 years, molecular-modelling tools have gradually gained a degree of acceptance in the pharmaceutical industry. Drug discovery has begun to benefit from physics-based simulations. While such simulations have great potential for improved molecular design, much scepticism remains about their value. The motivations for such reservations in industry and areas where simulations show promise for efficiency gains in preclinical research are discussed. In this, the first of two complementary papers, the scientific and technical progress that needs to be made to improve the predictive power of biomolecular simulations, and how this might be achieved, is firstly discussed (Part 1). In Part 2, the status of computer simulations in pharma is contrasted with aerodynamics modelling and weather forecasting, and comments are made on the cultural changes needed for equivalent computational technologies to become integrated into life-science industries.

Description: The SorC/DeoR family is a large family of bacterial transcription regulators that are involved in the control of carbohydrate metabolism and quorum sensing. To understand the structural basis of DNA recognition, structural studies of two functionally characterized SorC/DeoR family members from Bacillus subtilis were performed: the deoxyribonucleoside regulator bsDeoR and the central glycolytic genes regulator bsCggR. Each selected protein represents one of the subgroups that are recognized within the family. Crystal structures were determined of the N-terminal DNA-binding domains of bsDeoR and bsCggR in complex with DNA duplexes representing the minimal operator sequence at resolutions of 2.3 and 2.1 Å, respectively. While bsDeoRDBD contains a homeodomain-like HTH-type domain, bsCggRDBD contains a winged helix–turn–helix-type motif. Both proteins form C2-symmetric dimers that recognize two consecutive major grooves, and the protein–DNA interactions have been analyzed in detail. The crystal structures were used to model the interactions of the proteins with the full DNA operators, and a common mode of DNA recognition is proposed that is most likely to be shared by other members of the SorC/DeoR family.

Description: Data reduction and correction steps and processed data reproducibility in the emerging single-crystal total-scattering-based technique of three-dimensional differential atomic pair distribution function (3D-ΔPDF) analysis are explored. All steps from sample measurement to data processing are outlined using a crystal of CuIr2S4 as an example, studied in a setup equipped with a high-energy X-ray beam and a flat-panel area detector. Computational overhead as pertains to data sampling and the associated data-processing steps is also discussed. Various aspects of the final 3D-ΔPDF reproducibility are explicitly tested by varying the data-processing order and included steps, and by carrying out a crystal-to-crystal data comparison. Situations in which the 3D-ΔPDF is robust are identified, and caution against a few particular cases which can lead to inconsistent 3D-ΔPDFs is noted. Although not all the approaches applied herein will be valid across all systems, and a more in-depth analysis of some of the effects of the data-processing steps may still needed, the methods collected herein represent the start of a more systematic discussion about data processing and corrections in this field.

Description: Thyroglobulin is a homodimeric glycoprotein that is essential for the generation of thyroid hormones in vertebrates. Upon secretion into the lumen of follicles in the thyroid gland, tyrosine residues within the protein become iodinated to produce monoiodotyrosine (MIT) and diiodotyrosine (DIT). A subset of evolutionarily conserved pairs of DIT (and MIT) residues can then engage in oxidative coupling reactions that yield either thyroxine (T4; produced from coupling of a DIT `acceptor' with a DIT `donor') or triiodothyronine (T3; produced from coupling of a DIT acceptor with an MIT donor). Although multiple iodotyrosine residues have been identified as potential donors and acceptors, the specificity and structural context of the pairings (i.e. which donor is paired with which acceptor) have remained unclear. Here, single-particle cryogenic electron microscopy (cryoEM) was used to generate a high-resolution reconstruction of bovine thyroglobulin (2.3 Å resolution in the core region and 2.6 Å overall), allowing the structural characterization of two post-reaction acceptor–donor pairs as well as tyrosine residues modified as MIT and DIT. A substantial spatial separation between donor Tyr149 and acceptor Tyr24 was observed, suggesting that for thyroxine synthesis significant peptide motion is required for coupling at the evolutionarily conserved thyroglobulin amino-terminus.

Description: A new two-dimensional (2D) coordination polymer, namely, poly[[diaqua-[μ4-2,2′-[terephthaloylbis(azanediyl)]diacetato]calcium(II)] monohydrate], {[Ca(C12H10N2O6)(H2O)2]·H2O} n , (I), has been synthesized by the reaction of CaCl2 with 2,2′-[terephthaloylbis(azanediyl)]diacetic acid (H2 L). The title compound was structurally characterized by single-crystal X-ray diffraction analysis, elemental analysis and IR spectroscopy. In the crystal structure of (I), each CaII cation binds to six carboxylate groups from four symmetry-related L 2− dianions. The hexadentate L 2− ligand links four symmetry-related calcium cations into a 2D layer-like structure, which can be simplified as a uninodal SP 2-periodic (3,6)III net with the point symbol (43·63). In the lattice, all layers pack in parallel arrays through weak interlayer hydrogen bonding and π–π interactions. The thermal stability and photoluminescence properties of (I) have been investigated. Thermogravimetric analysis reveals the different thermal stabilities of the two coordinated water molecules due to their different hydrogen-bonding interactions. The title coordination polymer exhibits an excitation-wavelength-dependent fluorescence in the solid state.

Description: The self-assembly reaction of (+)-dibenzoyltartaric acid (D-H2DBTA) with 2,2′-bipyridine (bpy) and Mn(CH3CO2)2·4H2O yielded a new coordination polymer, namely, catena-poly[[[diaqua(2,2′-bipyridine-κ2 N,N′)manganese(II)]-μ-2,3-bis(benzoyloxy)butanedioato-κ2 O 2:O 3] dihydrate], {[Mn(C18H12O8)(C10H8N2)(H2O)2]·2H2O} n or {[Mn(DBTA)(bpy)(H2O)2]·2H2O} n , (I). Complex (I) has been characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis (TGA) and single-crystal and powder X-ray diffraction. It crystallizes in the orthorhombic space group P212121. In the complex, the Mn2+ cation displays a distorted octahedral {MnO4N2} geometry, formed from two carboxylate O atoms of two DBTA2− ligands, two cis-oriented N atoms from one chelating 2,2′-bipyridine ligand and two trans-oriented O atoms from coordinated water molecules. The polymer displays a 1D chain with an Mn...Mn distance of 9.428 (1) Å. Due to the presence of flexible polycarboxylate and rigid bipyridyl ligands in the molecular structure, a high thermal stability of the complex is attained. The magnetic properties of (I) were analyzed based on the mononuclear Mn2+ model due to the long intramolecular Mn...Mn distance. The zero field splitting (ZFS) contribution in the high-spin Mn2+ cation is almost negligible and there are weak antiferromagnetic couplings between 1D chains [zJ′ = −0.062 (5) cm−1], corresponding to an intermolecular Mn...Mn distance of 7.860 (2) Å.

Description: Four new solvates of the anti-HIV compound etravirine [systematic name: 4-({6-amino-5-bromo-2-[(4-cyanophenyl)amino]pyrimidin-4-yl}oxy)-3,5-dimethylbenzonitrile, C20H15BrN6O] with dimethyl sulfoxide (C2H6OS, two distinct monosolvates), 1,4-dioxane (C4H8O2, the 0.75-solvate) and N,N-dimethylacetamide (C4H9NO, the monosolvate), which exhibit conversion to the same anhydrous etravirine phase upon desolvation, and a stable etravirinium oxalate salt {6-amino-5-bromo-4-(4-cyano-2,6-dimethylphenoxy)-2-[(4-cyanophenyl)amino]pyrimidin-1-ium hemioxalate, C20H16BrN6O+·0.5C2O4 2−} were obtained. The crystal structures were solved by single-crystal X-ray diffraction and analyzed by powder X-ray diffraction, and the intermolecular interactions were explored by Hirshfeld surface analysis. Lattice energies were evaluated using the atom–atom force field Coulomb–London–Pauli (AA CLP) approximation, which distributes the total energy as four separate contributions: Coulombic, polarization, dispersion and repulsion. The formation of the solvates and the oxalate salt was further characterized by thermal analysis and IR spectroscopy.

Description: The effect of turbulence on snow precipitation is not incorporated into present weather forecasting models. Here we show evidence that turbulence is in fact a key influence on both fall speed and spatial distribution of settling snow. We consider three snowfall events under vastly different levels of atmospheric turbulence. We characterize the size and morphology of the snow particles, and we simultaneously image their velocity, acceleration and relative concentration over vertical planes approximately $30 extrm {m}^2$ in area. We find that turbulence-driven settling enhancement explains otherwise contradictory trends between the particle size and velocity. The estimates of the Stokes number and the correlation between vertical velocity and local concentration are consistent with the view that the enhanced settling is rooted in the preferential sweeping mechanism. When the snow vertical velocity is large compared to the characteristic turbulence velocity, the crossing trajectories effect results in strong accelerations. When the conditions of preferential sweeping are met, the concentration field is highly non-uniform and clustering appears over a wide range of scales. These clusters, identified for the first time in a naturally occurring flow, display the signature features seen in canonical settings: power-law size distribution, fractal-like shape, vertical elongation and large fall speed that increases with the cluster size. These findings demonstrate that the fundamental phenomenology of particle-laden turbulence can be leveraged towards a better predictive understanding of snow precipitation and ground snow accumulation. They also demonstrate how environmental flows can be used to investigate dispersed multiphase flows at Reynolds numbers not accessible in laboratory experiments or numerical simulations.

Description: The molecular orbitals (MOs) of diformohydrazide have been determined from the electron density measured by X-ray diffraction. The experimental and refinement procedures are explained in detail and the validity of the obtained MOs is assessed from the crystallographic point of view. The X-ray structure factors were measured at 100 K by a four-circle diffractometer avoiding multiple diffraction, the effect of which on the structure factors is comparable to two-centre structure factors. There remained no significant peaks on the residual density map and the R factors reduced significantly. Among the 788 MO coefficients, 731 converged, of which 694 were statistically significant. The C—H and N—H bond distances are 1.032 (2) and 1.033 (3) Å, respectively. The electron densities of theoretical and experimental MOs and the differences between them are illustrated. The overall features of the electron density obtained by X-ray molecular orbital (XMO) analysis are in good agreement with the canonical orbitals calculated by the restricted Hartree Fock (RHF) method. The bonding-electron distribution around the middle of each bond is well represented and the relative phase relationships of the π orbitals are reflected clearly in the electron densities on the plane perpendicular to the molecular plane. However, differences are noticeable around the O atom on the molecular plane. The orbital energies obtained by XMO analysis are about 0.3 a.u. higher than the corresponding canonical orbitals, except for MO10 to MO14 which are about 0.7 a.u. higher. These exceptions are attributed to the N—H...O′′ intermolecular hydrogen bond, which is neglected in the MO models of the present study. The hydrogen bond is supported by significant electron densities at the saddle points between the H(N) and O′′ atoms in MO7, 8, 14 and 17, and by that of O′′-p extended over H(N) in MO21 and 22, while no peaks were found in MO10, 11, 13 and 15. The electron density of each MO clearly exhibits its role in the molecule. Consequently, the MOs obtained by XMO analysis give a fundamental quantum mechanical insight into the real properties of molecules.

Description: The concepts of `wavevector star channel' and `wavevector star channel group' are newly defined, which allow the effective study of phase transitions considering directly the translational symmetry breaking in crystals. A method is suggested by which the wavevector star channels can be found using the image of the representation of the translational group. According to this method, the wavevector star channels are found for the 80 Lifschitz stars in the reciprocal lattice. The wavevector star channel group is defined as the set of symmetry elements of the parent phase which leave the star channel invariant, and the wavevector star channel groups with one, two, three and four arms are calculated. It is shown that the complicated symmetry changes in the pyroelectric crystal Pb1−x Ca x TiO3 (PCT) can be described using the new five-component reducible order parameter transformed according to the representation of the wavevector star channel group, rather than the nine-component one based on the theory of the full irreducible representation of the space group.

Description: To decompose a wide-angle X-ray diffraction (WAXD) curve of a semi-crystalline polymer into crystalline peaks and amorphous halos, a theoretical best-fitted curve, i.e. a mathematical model, is constructed. In fitting the theoretical curve to the experimental one, various functions can be used to quantify and minimize the deviations between the curves. The analyses and calculations performed in this work have proved that the quality of the model, its parameters and consequently the information on the structure of the investigated polymer are considerably dependent on the shape of an objective function. It is shown that the best models are obtained employing the least-squares method in which the sum of squared absolute errors is minimized. On the other hand, the methods in which the objective functions are based on the relative errors do not give a good fit and should not be used. The comparison and evaluation were performed using WAXD curves of seven polymers: isotactic polypropylene, polyvinylidene fluoride, cellulose I, cellulose II, polyethylene, polyethylene terephthalate and polyamide 6. The methods were compared and evaluated using statistical tests and measures of the quality of fitting.

Description: According to Löwenstein's rule, Al–O–Al bridges are forbidden in the aluminosilicate framework of zeolites. A graph-theoretical interpretation of the rule, based on the concept of independent sets, was proposed earlier. It was shown that one can apply the vector method to the associated periodic net and define a maximal Al/(Al+Si) ratio for any aluminosilicate framework following the rule; this ratio was called the independence ratio of the net. According to this method, the determination of the independence ratio of a periodic net requires finding a subgroup of the translation group of the net for which the quotient graph and a fundamental transversal have the same independence ratio. This article and a companion paper deal with practical issues regarding the calculation of the independence ratio of mainly 2-periodic nets and the determination of site distributions realizing this ratio. The first paper describes a calculation technique based on propositional calculus and introduces a multivariate polynomial, called the independence polynomial. This polynomial can be calculated in an automatic way and provides the list of all maximal independent sets of the graph, hence also the value of its independence ratio. Some properties of this polynomial are discussed; the independence polynomials of some simple graphs, such as short paths or cycles, are determined as examples of calculation techniques. The method is also applied to the determination of the independence ratio of the 2-periodic net dhc.

Description: Starting from the Boltzmann–Enskog kinetic equations, the charge transport equation for bidisperse granular flows with contact electrification is derived with separate mean velocities, total kinetic energies, charges and charge variances for each solid phase. To close locally averaged transport equations, a Maxwellian distribution is presumed for both particle velocity and charge. The hydrodynamic equations for bidisperse solid mixtures are first revisited and the resulting model consisting of the transport equations of mass, momentum, total kinetic energy, which is the sum of the granular temperature and the trace of fluctuating kinetic tensor, and charge is then presented. The charge transfer between phases and the charge build-up within a phase are modelled with local charge and effective work function differences between phases and the local electric field. The revisited hydrodynamic equations and the derived charge transport equation with constitutive relations are assessed through hard-sphere simulations of three-dimensional spatially homogeneous, quasi-one-dimensional spatially inhomogeneous bidisperse granular gases and a three-dimensional segregating bidisperse granular flow with conducting walls.

Description: Particle–wall interactions have broad biological and technological applications. In particular, some artificial microswimmers capitalize on their translation–rotation coupling near a wall to generate directed propulsion. Emerging biomedical applications of these microswimmers in complex biological fluids prompt questions on the impact of non-Newtonian rheology on their propulsion. In this work, we report some intriguing effects of shear-thinning rheology, a ubiquitous non-Newtonian behaviour of biological fluids, on the translation–rotation coupling of a particle near a wall. One particularly interesting feature revealed here is that the wall-induced translation by rotation can occur in a direction opposite to what might be intuitively expected for an object rolling on a solid substrate. We elucidate the underlying physical mechanism and discuss its implications on the design of micromachines and bacterial motion near walls in complex fluids.

Description: The section of the Bilbao Crystallographic Server (https://www.cryst.ehu.es/) dedicated to subperiodic groups contains crystallographic and Brillouin-zone databases for the layer groups. The crystallographic databases include the generators/general positions (GENPOS), Wyckoff positions (WYCKPOS) and maximal subgroups (MAXSUB). The Brillouin-zone database (LKVEC) offers k-vector tables and Brillouin-zone figures of all 80 layer groups which form the background of the classification of their irreducible representations. The symmetry properties of the wavevectors are described applying the so-called reciprocal-space-group approach and this classification scheme is compared with that of Litvin & Wike [(1991), Character Tables and Compatibility Relations of the Eighty Layer Groups and Seventeen Plane Groups. New York: Plenum Press]. The specification of independent parameter ranges of k vectors in the representation domains of the Brillouin zones provides a solution to the problems of uniqueness and completeness of layer-group representations. The Brillouin-zone figures and k-vector tables are described in detail and illustrated by several examples.

Description: We study the reactive displacement of two miscible fluids in channel flows and establish a quantitative link between fluid stretching and chemical reactivity. At the mixing interface, the two fluids react according to the instantaneous irreversible bimolecular reaction $A + B ightarrow C$ . We simulate the advection–diffusion–reaction problem using a random walk based reactive particle method that is free of numerical dispersion. The relative contributions of stretching and diffusion to mixing-limited reaction is controlled by changing the Péclet number, and the channel roughness is also systematically varied. We observe optimal ranges of fluid stretching that maximize reactivity, which are captured by a Lagrangian stretching measure based on an effective time period that honours the stretching history. We show that the optimality originates from the competition between the enhanced mixing by fluid stretching and the mass depletion of the reactants. We analytically derive the spatial distribution of reaction products using a lamellar formulation and successfully predict the optimal ranges of fluid stretching, which are consistent across different levels of channel roughness. These findings provide a mechanistic understanding of how the interplay between fluid stretching, diffusion and channel roughness controls mixing-limited reactions in rough channel flows, and show how reaction hot spots can be predicted from the concept of optimal fluid stretching.

Description: Direct numerical simulations (DNS) of oscillatory flow around a cylinder show that the Stokes–Wang (S–W) solution agrees exceptionally well with DNS results over a much larger parameter space than the constraints of $ eta K^2ll 1$ and $ eta gg 1$ specified by the S–W solution, where $K$ is the Keulegan–Carpenter number and $ eta$ is the Stokes number. The ratio of drag coefficients predicted by DNS and the S–W solution, $varLambda _K$ , mapped out in the $Kext {--} eta$ space, shows that $varLambda _K 〈 1.05$ for $Kleq {sim }0.8$ and $1 leq eta leq 10^6$ , which contradicts its counterpart based on experimental results. The large $varLambda _K$ values are primarily induced by the flow separation on the cylinder surface, rather than the development of three-dimensional (Honji) instabilities. The difference between two-dimensional and three-dimensional DNS results is less than 2 % for $K$ smaller than the corresponding $K$ values on the iso-line of $varLambda _K = 1.1$ with $ eta = 200ext {--}20,950$ . The flow separation actually occurs over the parameter space where $varLambda _Kapprox 1.0$ . It is the spatio-temporal extent of flow separation rather than separation itself that causes large $varLambda _K$ values. The proposed measure for the spatio-temporal extent, which is more sensitive to $K$ than $ eta$ , correlates extremely well with $varLambda _K$ . The conventional Morison equation with a quadratic drag component is fundamentally incorrect at small $K$ where the drag component is linearly proportional to the incoming velocity with a phase difference of ${ m pi} /4$ . A general form of the Morison equation is proposed by considering both viscous and form drag components and demonstrated to be superior to the conventional equation for $K 〈 {sim }2.0$ .

Description: We investigate the effect of helicity on the scale-similar structures of homogeneous isotropic and non-mirror-symmetric turbulence based on the Lagrangian renormalised approximation (LRA), which is a self-consistent closure theory proposed by Kaneda (J. Fluid Mech., vol. 107, 1981, pp. 131–145). In this study, we focus on the time scale representing the scale-similar range. For the LRA, the Lagrangian two-time velocity correlation and response function determine the representative time scale. The LRA predicts that both the Lagrangian two-time velocity correlation and response function equation do not explicitly depend on helicity. We assume the extended scale-similar spectra and time scale by considering the helicity dissipation rate. Considering the small-scale structures, the requirements for the energy and helicity fluxes and response function equation to be scale similar, yield the conventional inertial-range power laws and provide the energy and helicity spectra $propto k^{-5/3}$ and the time scale $propto varepsilon ^{-1/3} k^{-2/3}$ , where $varepsilon$ and $k$ denote the energy dissipation rate and wavenumber, respectively. Notably, energy flux can be scale similar only when $k^H /k ll 1$ , where $k^H = varepsilon ^H/varepsilon$ and $varepsilon ^H$ denotes the helicity dissipation rate. This condition makes the energy cascade process in the scale-similar range completely independent of helicity. We also investigate the localness of the interscale interaction in the energy and helicity cascades for the LRA. We demonstrate that the helicity cascade is slightly non-local in scales compared with the energy cascade. This study provides a foundation on the modelling of non-mirror-symmetric turbulent flows.

Description: The modelling of natural convection in porous media is receiving increased interest due to its significance in environmental and engineering problems. State-of-the-art simulations are based on the classic macroscopic Darcy–Oberbeck–Boussinesq (DOB) equations, which are widely accepted to capture the underlying physics of convection in porous media provided the Darcy number, $Da$ , is small. In this paper we analyse and extend the recent pore-resolved direct numerical simulations (DNS) of Gasow et al. (J. Fluid Mech, vol. 891, 2020, p. A25) and show that the macroscopic diffusion, which is neglected in DOB, is of the same order (with respect to $Da$ ) as the buoyancy force and the Darcy drag. Consequently, the macroscopic diffusion must be modelled even if the value of $Da$ is small. We propose a ‘two-length-scale diffusion’ model, in which the effect of the pore scale on the momentum transport is approximated with a macroscopic diffusion term. This term is determined by both the macroscopic length scale and the pore scale. It includes a transport coefficient that solely depends on the pore-scale geometry. Simulations of our model render a more accurate Sherwood number, root mean square (r.m.s.) of the mass concentration and r.m.s. of the velocity than simulations that employ the DOB equations. In particular, we find that the Sherwood number $Sh$ increases with decreasing porosity and with increasing Schmidt number $(Sc)$ . In addition, for high values of $Ra$ and high porosities, $Sh$ scales nonlinearly. These trends agree with the DNS, but are not captured in the DOB simulations.

Description: The novel hemilabile ferrocenylbisphosphane 1,1′-bis(bis{2-[(dimethylamino)methyl]phenyl}phosphanyl)ferrocene, [Fe{C5H4P(C6H4CH2NMe2-o)2}2] (1), was synthesized by reacting bis(dichlorophosphanyl)ferrocene, [Fe{C5H4(PCl2)}2] with LiC6H4CH2NMe2-o. Treatment of 1 with gray selenium and anhydrous ZnCl2 yielded, respectively, the bisselenide (ferrocene-1,1′-diyl)bis(bis{2-[(dimethylamino)methyl]phenyl}phosphine selenide), [Fe(C23H28N2PSe)2] (2), and the dizinc complex [μ-1,1′-bis(bis{2-[(dimethylamino)methyl]phenyl}phosphanyl)ferrocene-κ2 N,P:κ2 N′,P′]bis[dichloridozinc(II)] dichloromethane monosolvate, [FeZn2Cl4(C23H28N2P)2]·CH2Cl2 (3), and both have been structurally characterized. Both compounds crystallized with the asymmetric unit containing half a molecule and with the Fe atom on an inversion centre. A Hirshfeld surface analysis indicated that the most significant contributions to the crystal packing of 2 are from H...H (76.7%), C...H/H...C (13.2%) and Se...H/H...Se (7.1%) contacts, while those for 3 are from H...H (62.3%), Cl...H/H...Cl (24.4%) and C...H/H...C (10.9%) contacts.

Description: When calculating derivatives of structure factors, there is one particular term (the derivatives of the atomic form factors) that will always be zero in the case of tabulated spherical atomic form factors. What happens if the form factors are non-spherical? The assumption that this particular term is very close to zero is generally made in non-spherical refinements (for example, implementations of Hirshfeld atom refinement or transferable aspherical atom models), unless the form factors are refinable parameters (for example multipole modelling). To evaluate this general approximation for one specific method, a numerical differentiation was implemented within the NoSpherA2 framework to calculate the derivatives of the structure factors in a Hirshfeld atom refinement directly as accurately as possible, thus bypassing the approximation altogether. Comparing wR 2 factors and atomic parameters, along with their uncertainties from the approximate and numerically differentiating refinements, it turns out that the impact of this approximation on the final crystallographic model is indeed negligible.

Description: The capability to obtain essential nutrients in hostile environments is a critical skill for pathogens. Under zinc-deficient conditions, Pseudomonas aeruginosa expresses a pool of metal homeostasis control systems that is complex compared with other Gram-negative bacteria and has only been partially characterized. Here, the structure and zinc-binding properties of the protein PA4063, the first component of the PA4063–PA4066 operon, are described. PA4063 has no homologs in other organisms and is characterized by the presence of two histidine-rich sequences. ITC titration detected two zinc-binding sites with micromolar affinity. Crystallographic characterization, performed both with and without zinc, revealed an α/β-sandwich structure that can be classified as a noncanonical ferredoxin-like fold since it differs in size and topology. The histidine-rich stretches located at the N-terminus and between β3 and β4 are disordered in the apo structure, but a few residues become structured in the presence of zinc, contributing to coordination in one of the two sites. The ability to bind two zinc ions at relatively low affinity, the absence of catalytic cavities and the presence of two histidine-rich loops are properties and structural features which suggest that PA4063 might play a role as a periplasmic zinc chaperone or as a concentration sensor useful for optimizing the response of the pathogen to zinc deficiency.

Description: Protein crystallization has for decades been a critical and restrictive step in macromolecular structure determination via X-ray diffraction. Crystallization typically involves a multi-stage exploration of the available chemical space, beginning with an initial sampling (screening) followed by iterative refinement (optimization). Effective screening is important for reducing the number of optimization rounds required, reducing the cost and time required to determine a structure. Here, an initial screen (Shotgun II) derived from analysis of the up-to-date Protein Data Bank (PDB) is proposed and compared with the previously derived (2014) Shotgun I screen. In an update to that analysis, it is clarified that the Shotgun approach entails finding the crystallization conditions that cover the most diverse space of proteins by sequence found in the PDB, which can be mapped to the well known maximum coverage problem in computer science. With this realization, it was possible to apply a more effective algorithm for selecting conditions. In-house data demonstrate that compared with alternatives, the Shotgun I screen has been remarkably successful over the seven years that it has been in use, indicating that Shotgun II is also likely to be a highly effective screen.

Description: Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis (NpSRII–NpHtrII) was performed. The influence of the polydispersity of NpSRII–NpHtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.

Description: Debranching is a critical step in the mobilization of the important energy store glycogen. In eukaryotes, including fungi and animals, the highly conserved glycogen-debranching enzyme (GDE) debranches glycogen by a glucanotransferase (GT) reaction followed by a glucosidase (GC) reaction. Previous work indicated that these reactions are catalyzed by two active sites located more than 50 Å apart and provided insights into their catalytic mechanisms and substrate recognition. Here, five crystal structures of GDE in complex with oligosaccharides with 4–9 glucose residues are presented. The data suggest that the glycogen main chain plays a critical role in binding to the GT and GC active sites of GDE and that a minimum of five main-chain residues are required for optimal binding.

Description: The enzyme hydroxymethylbilane synthase (HMBS; EC 4.3.1.8), also known as porphobilinogen deaminase, catalyses the stepwise addition of four molecules of porphobilinogen to form the linear tetrapyrrole 1-hydroxymethylbilane. Thirty years of crystal structures are surveyed in this topical review. These crystal structures aim at the elucidation of the structural basis of the complex reaction mechanism involving the formation of tetrapyrrole from individual porphobilinogen units. The consistency between the various structures is assessed. This includes an evaluation of the precision of each molecular model and what was not modelled. A survey is also made of the crystallization conditions used in the context of the operational pH of the enzyme. The combination of 3D structural techniques, seeking accuracy, has also been a feature of this research effort. Thus, SAXS, NMR and computational molecular dynamics have also been applied. The general framework is also a considerable chemistry research effort to understand the function of the enzyme and its medical pathologies in acute intermittent porphyria (AIP). Mutational studies and their impact on the catalytic reaction provide insight into the basis of AIP and are also invaluable for guiding the understanding of the crystal structure results. Future directions for research on HMBS are described, including the need to determine the protonation states of key amino-acid residues identified as being catalytically important. The question remains – what is the molecular engine for this complex reaction? Thermal fluctuations are the only suggestion thus far.

Description: Protein salting-out is a well established phenomenon that in many cases leads to amorphous structures and protein gels, which are usually not considered to be useful for protein structure determination. Here, microstructural measurements of several different salted-out protein dense phases are reported, including of lysozyme, ribonuclease A and an IgG1, showing that salted-out protein gels unexpectedly contain highly ordered protein nanostructures that assemble hierarchically to create the gel. The nanocrystalline domains are approximately 10–100 nm in size, are shown to have structures commensurate with those of bulk crystals and grow on time scales in the order of an hour to a day. Beyond revealing the rich, hierarchical nanoscale to mesoscale structure of protein gels, the nanocrystals that these phases contain are candidates for structural biology on next-generation X-ray free-electron lasers, which may enable the study of biological macromolecules that are difficult or impossible to crystallize in bulk.