Twin Refinement Research Articles

Synthesis and crystal structure of diisothiocyanatotetrakis(4-methylpyridine N-oxide)cobalt(II) and diisothiocyanatotris(4-methylpyridine N-oxide)cobalt(II) showing two different metal coordination polyhedra

The reaction of Co(NCS)2 with 4-methylpyridine N-oxide (C6H7NO) leads to the formation of two compounds, namely, tetrakis(4-methylpyridine N-oxide-κO)bis(thiocyanato-κN)cobalt(II), [Co(NCS)2(C6H7NO)4] (1), and tris(4-methylpyridine N-oxide-κO)bis(thiocyanato-κN)cobalt(II), [Co(NCS)2(C6H7NO)3] (2). The asymmetric unit of 1 consists of one CoII cation located on a centre of inversion, as well as one thiocyanate anion and two 4-methylpyridine N-oxide coligands in general positions. The CoII cations are octahedrally coordinated by two terminal N-bonding thiocyanate anions in trans positions and four 4-methylpyridine N-oxide ligands. In the extended structure, these complexes are linked by C—H...O and C—H...S interactions. In compound 2, two crystallographically independent complexes are present, which occupy general positions. In each of these complexes, the CoII cations are coordinated in a trigonal–bipyramidal manner by two terminal N-bonding thiocyanate anions in axial positions and by three 4-methylpyridine N-oxide ligands in equatorial positions. In the crystal, these complex molecules are linked by C—H...S interactions. For compound 2, a nonmerohedral twin refinement was performed. Powder X-ray diffraction (PXRD) reveals that 2 was nearly obtained as a pure phase, which is not possible for compound 1. Differential thermoanalysis and thermogravimetry data (DTA–TG) show that compound 2 start to decompose at about 518 K.

Friction stir welding of CoCrNi medium-entropy alloy: Recrystallization behaviour and strengthening mechanism

Dynamic recrystallization (DRX), deformation-induced mechanical twins, and strengthening mechanism of CoCrNi equi-atomic medium-entropy alloy (MEA), welded by friction stir welding (FSW) at different welding speeds, were systematically investigated in this study. The results indicated that FSW led to grain refinement in the stir zones (SZs) with diameters fluctuating in the range of 2.1–9.6 μm. The hardness was improved from ∼154HV (base material, BM) to 238–263HV (SZ) by FSW. The yield strength and ultimate tensile strength of the optimal SZs were 601 MPa and 844 MPa, respectively, which were 260% and 134% higher than those of the as-received material, respectively. Analyses of DRX behaviour indicated that discontinuous DRX (DDRX), continuous DRX (CDRX), and geometric DRX (GDRX) were successively activated with increasing strain during FSW to facilitate grain refinement. The larger the grain size, the higher the fraction of mechanical twins. However, the thickness of the twins had a negative correlation with the grain size. Although a few HCP structures were formed on the twin boundaries, grain refinement and dislocation hardening mechanisms remained dominant in enhancing the mechanical properties of the SZs. The strength-ductility synergy by FSW, under low heat input conditions, was caused by the formation of thin mechanical twins in fine equiaxed grains. Thinner twins were more effective in transferring and homogenising plastic deformation, thereby contributing to the postponing of plastic instability and further promoting an excellent combination of strength and ductility. These findings confirm that FSW is a promising approach for strengthening the MEA for superior performance.

Crystal structure of bis-(N,N'-di-methyl-thio-urea-κS)bis-(thio-cyanato-κN)cobalt(II).

During systematic investigations on the synthesis of coordination polymers with Co(NCS)2 involving different thio-urea derivatives as coligands, crystals of the title compound Co(NCS)2(N,N'-di-methyl-thio-urea)2, or [Co(C3H8N2S)2(NCS)2], were obtained. These crystals were non-merohedric twins and therefore, a twin refinement using data in HKLF-5 format was performed. In the crystal structure of this compound, the CoII cations are coordinated by two N-terminally bonded thio-cyanate anions as well as two S-bonding N,N'-di-methyl-thio-urea mol-ecules, forming two crystallographically independent discrete complexes each with a strongly distorted tetra-hedral geometry. An intricate network of inter-molecular N-H⋯S and C-H⋯S hydrogen bonds can be found between the complexes. The thermogravimetric curve of the title compound shows two discrete steps in which all coligand mol-ecules have been emitted, which is also accompanied by partial decomposition of the cobalt thio-cyanate. If the measurement is stopped after the first mass loss, only broad reflections of CoS can be found in the XRPD pattern of the residue, which proves that this compound decomposes completely upon heating. However, at lower temperatures an endothermic signal can be found in the DTA and DSC curve, which corresponds to melting, as proven by thermomicroscopy.

Synthesis and crystal structure of (1,4,7,10-tetra-aza-cyclo-dodecane-κ4 N)(tetra-sulfido-κ2 S 1,S 4)manganese(II).

The title compound, [Mn(S4)(C8H20N4)], was accidentally obtained by the hydro-thermal reaction of Mn(ClO4)2·6H2O, cyclen (cyclen = 1,4,7,10-tetra-aza-cyclo-dodeca-ne) and Na3SbS4·9H2O in water at 413 K, indicating that polysulfide anions might represent inter-mediates in the synthesis of thio-metallate compounds using Na3SbS4·9H2O as a reactant. X-ray powder diffraction proves that the sample is slightly contaminated with NaSb(OH)6 and an unknown crystalline phase. The crystal investigated was twinned with a twofold rotation axis as the twin element, and therefore a twin refinement using data in HKLF-5 format was performed. The asymmetric unit of the title compound consists of one MnII cation, one [S4]2- anion and one cyclen ligand in general positions. The MnII cation is sixfold coordinated by two cis-S atoms of the [S4]2- anions, as well as four N atoms of the cyclen ligand within an irregular coordination. The complexes are linked via pairs of N-H⋯S hydrogen bonds into chains, which are further linked into layers by additional N-H⋯S hydrogen bonding. These layers are connected into a three-dimensional network by inter-molecular N-H⋯S and C-H⋯S hydrogen bonding. It is noted that only one similar complex with MnII is reported in the literature.

Synthesis and crystal structure of catena-poly[[bis[(2,2';6',2''-terpyridine)-manganese(II)]-μ4-penta-thio-dianti-monato] tetra-hydrate] showing a 1D MnSbS network.

The asymmetric unit of the title compound, {[Mn2Sb2S5(C15H11N3)2]·4H2O} n , consists of two crystallographically independent MnII ions, two unique terpyridine ligands, one [Sb2S5]4- anion and four solvent water mol-ecules, all of which are located in general positions. The [Sb2S5]4- anion consists of two SbS3 units that share common corners. Each of the MnII ions is fivefold coordinated by two symmetry-related S atoms of [Sb2S5]4- anions and three N atoms of a terpyridine ligand within an irregular coordination. Each two anions are linked by two [Mn(terpyridine)]2+ cations into chains along the c-axis direction that consist of eight-membered Mn2Sb2S4 rings. These chains are further connected into a three-dimensional network by inter-molecular O-H⋯O and O-H⋯S hydrogen bonds. The crystal investigated was twinned and therefore, a twin refinement using data in HKLF-5 [Sheldrick (2015 ▸). Acta Cryst. C71, 3-8] format was performed.

Fine-grained processing and electron backscatter diffraction (EBSD) analysis of cold-rolled Inconel 617

Fine-grained processing of Inconel 617 sheet was proposed, and microstructural evolution during processing was analyzed. The optimum recovery temperature at 750 °C and the best recrystallization annealing temperature at 1000 °C were determined by experiments. The optimal fine-grained process comprised heat treatment (750 °C × 1 h), first cold rolling (60% reduction rate), high-temperature recovery (750 °C × 1 h), second cold rolling (10% reduction rate), and recrystallization annealing (1000 °C × 3 h). After recrystallization annealing (1000 °C × 3 h), the fine-grained sheet consisted of equiaxed grains with a size of 4–6 μm. A high proportion of high-angle grain boundaries was observed, and most of the grain orientation spread values were less than 1. The grain recrystallized completely. Twin refinement mechanism played a dominant role in sheet grain refinement. The hardness and tensile mechanical properties of the fine-grained sheet were notably stronger than those of the original sheet.

Branching of {110) twin boundaries in five-layered Ni-Mn-Ga bent single crystals

Two bending tests around two perpendicular axes were applied to 10M Ni-Mn-Ga single crystals with five-layered modulated structure. The crystal structure and microstructure evolution were examined using synchrotron radiation and electron backscatter diffraction, respectively. The bend stress results in pseudoelasto-plastic strain due to {101) twins tapering. A close examination of the microstructure reveals an additional pattern indicating microstructural changes in the form of {110) twins. As bending proceeds the {110) twins branch undergoing a significant twin refinement. Additionally, an elastic change of lattice parameters is confirmed yielding a higher total pseudoelastic strain. Unloading restores the initial twin configuration removing a large amount of the {110) twin boundaries, however, this process is followed by incomplete recovery since the samples do not retain its original shape entirely. The paper underlines the differences in mechanism for bending around two perpendicular axes explaining the amount of strain observed under pseudoelastic deformation. Additionally, the results are discussed with respect to minimization of elastic energy due to twin refinement and branching as well as mobility of the {101) and {110) twin boundaries.

An empirical correction for the influence of low-energy contamination

Low-energy contamination caused by focusing multilayer optics has been known for a long time. So far, the only method to avoid this problem is attenuation by interposition of a low-density material foil into the beam. However, attenuation lowers the intensity, which might be crucial, especially for charge density data collection, and is of course not possible for already measured data. In this article, an empirical correction is proposed as an alternative or addition. The low-energy contamination mainly affects the reflections with indices 3h3k3l. In the programSADABS, a 3λ correction in analogy to the earlier 2/λ correction is now implemented. The correction factor can be determined from the model, but for most cases, a default value depending on the experimental settings is acceptable. Alternatively, the correction can be refined inSHELXL, similarly to a twin refinement. An investigation of several data sets collected with and without attenuation revealed that the empirical correction and attenuation lead to similar improvements. The empirical correction is of special interest for charge density investigations, where the loss of intensity could hinder the data collection up to very high resolution. Here, the improvements in the model, especially for the noise level of the residual density, are even more pronounced.

Crystal structure of borated N,N,N',N'-tetra-methyldi-amino-methane.

In the title compound, {[(di­methyl­amino)­meth­yl]di­methyl­amine}­trihydridoboron, C5H17BN2, the tetra­hedral geometry of the N—C—N unit is slightly disorted. As a result of the bulky amine substituents, a wider N—C—N angle of 113.6 (1)° is observed. The bond lengths between the N atom and methyl groups are slighly elongated to 1.481 (2) and 1.482 (2) Å at the borated N atom, whereas the distances between the other N atom and its methyl groups are only 1.461 (2) and 1.462 (2) Å. The studied crystal was twinned. The twin data refinement was subsequently carried out with a scale factor of 0.263 (1). The two lattices of the twin domains were rotated by 179.84°.

Gd4(BO2)O5F – a gadolinium borate fluoride oxide comprising a linear BO2 moiety

Abstract Gadolinium borate fluoride oxide Gd4(BO2)O5F crystallises in space group Pmmn (no. 59, a = 1574.6(4), b = 381.42(7), c = 660.88(11) pm, 565 refl., 28 parameters, R 1 = 0.039, wR 2 = 0.128, twin refinement) and comprises linear BO2 − anions between closely packed [GdO] layers formed by OGd4 tetrahedra and terminated by oxygen and fluorine atoms. The crystal structure’s relationship with the NiAs type is illustrated. The Raman spectrum recorded on a single crystal of Gd4(BO2)O5F comprises a single peak at 1364 cm−1 assigned to the only Raman-active vibrational mode ν s of the linear triatomic O–B–O units besides very weak peaks at 805 and 2083 cm−1 (presumably the respective δ and ν as modes).

Identification of Biochemically Distinct Properties of the Small Ubiquitin-related Modifier (SUMO) Conjugation Pathway in Plasmodium falciparum

Small ubiquitin-related modifiers (SUMOs) are post-translationally conjugated to other proteins and are thereby essential regulators of a wide range of cellular processes. Sumoylation, and enzymes of the sumoylation pathway, are conserved in the malaria causing parasite, Plasmodium falciparum. However, the specific functions of sumoylation in P. falciparum, and the degree of functional conservation between enzymes of the human and P. falciparum sumoylation pathways, have not been characterized. Here, we demonstrate that sumoylation levels peak during midstages of the intra-erythrocyte developmental cycle, concomitant with hemoglobin consumption and elevated oxidative stress. In vitro studies revealed that P. falciparum E1- and E2-conjugating enzymes interact effectively to recognize and modify RanGAP1, a model mammalian SUMO substrate. However, in heterologous reactions, P. falciparum E1 and E2 enzymes failed to interact with cognate human E2 and E1 partners, respectively, to modify RanGAP1. Structural analysis, binding studies, and functional assays revealed divergent amino acid residues within the E1-E2 binding interface that define organism-specific enzyme interactions. Our studies identify sumoylation as a potentially important regulator of oxidative stress response during the P. falciparum intra-erythrocyte developmental cycle, and define E1 and E2 interactions as a promising target for development of parasite-specific inhibitors of sumoylation and parasite replication.

Structural Basis of the Interaction of MbtH-like Proteins, Putative Regulators of Nonribosomal Peptide Biosynthesis, with Adenylating Enzymes

The biosynthesis of nonribosomally formed peptides (NRPs), which include important antibiotics such as vancomycin, requires the activation of amino acids through adenylate formation. The biosynthetic gene clusters of NRPs frequently contain genes for small, so-called MbtH-like proteins. Recently, it was discovered that these MbtH-like proteins are required for some of the adenylation reactions in NRP biosynthesis, but the mechanism of their interaction with the adenylating enzymes has remained unknown. In this study, we determined the structure of SlgN1, a 3-methylaspartate-adenylating enzyme involved in the biosynthesis of the hybrid polyketide/NRP antibiotic streptolydigin. SlgN1 contains an MbtH-like domain at its N terminus, and our analysis defines the parameters required for an interaction between MbtH-like domains and an adenylating enzyme. Highly conserved tryptophan residues of the MbtH-like domain critically contribute to this interaction. Trp-25 and Trp-35 form a cleft on the surface of the MbtH-like domain, which accommodates the alanine side chain of Ala-433 of the adenylating domain. Mutation of Ala-433 to glutamate abolished the activity of SlgN1. Mutation of Ser-23 of the MbtH-like domain to tyrosine resulted in strongly reduced activity. However, the activity of this S23Y mutant could be completely restored by addition of the intact MbtH-like protein CloY from another organism. This suggests that the interface found in the structure of SlgN1 is the genuine interface between MbtH-like proteins and adenylating enzymes.

Twin refinement withJANA2006: from polytypism to modulated phases

Twin refinement with<i>JANA2006</i>: from polytypism to modulated phases

Structure of Cinaciguat (BAY 58–2667) Bound to Nostoc H-NOX Domain Reveals Insights into Heme-mimetic Activation of the Soluble Guanylyl Cyclase

Heme is a vital molecule for all life forms with heme being capable of assisting in catalysis, binding ligands, and undergoing redox changes. Heme-related dysfunction can lead to cardiovascular diseases with the oxidation of the heme of soluble guanylyl cyclase (sGC) critically implicated in some of these cardiovascular diseases. sGC, the main nitric oxide (NO) receptor, stimulates second messenger cGMP production, whereas reactive oxygen species are known to scavenge NO and oxidize/inactivate the heme leading to sGC degradation. This vulnerability of NO-heme signaling to oxidative stress led to the discovery of an NO-independent activator of sGC, cinaciguat (BAY 58-2667), which is a candidate drug in clinical trials to treat acute decompensated heart failure. Here, we present crystallographic and mutagenesis data that reveal the mode of action of BAY 58-2667. The 2.3-A resolution structure of BAY 58-2667 bound to a heme NO and oxygen binding domain (H-NOX) from Nostoc homologous to that of sGC reveals that the trifurcated BAY 58-2667 molecule has displaced the heme and acts as a heme mimetic. Carboxylate groups of BAY 58-2667 make interactions similar to the heme-propionate groups, whereas its hydrophobic phenyl ring linker folds up within the heme cavity in a planar-like fashion. BAY 58-2667 binding causes a rotation of the alphaF helix away from the heme pocket, as this helix is normally held in place via the inhibitory His(105)-heme covalent bond. The structure provides insights into how BAY 58-2667 binds and activates sGC to rescue heme-NO dysfunction in cardiovascular diseases.

X-ray analysis of bilirubin oxidase from Myrothecium verrucaria at 2.3 A resolution using a twinned crystal.

Bilirubin oxidase (BOD), a multicopper oxidase found in Myrothecium verrucaria, catalyzes the oxidation of bilirubin to biliverdin. Oxygen is the electron acceptor and is reduced to water. BOD is used for diagnostic analysis of bilirubin in serum and has attracted considerable attention as an enzymatic catalyst for the cathode of biofuel cells that work under neutral conditions. Here, the crystal structure of BOD is reported for the first time. Blue bipyramid-shaped crystals of BOD obtained in 2-methyl-2,4-pentanediol (MPD) and ammonium sulfate solution were merohedrally twinned in space group P6(3). Structure determination was achieved by the single anomalous diffraction (SAD) method using the anomalous diffraction of Cu atoms and synchrotron radiation and twin refinement was performed in the resolution range 33-2.3 A. The overall organization of BOD is almost the same as that of other multicopper oxidases: the protein is folded into three domains and a total of four copper-binding sites are found in domains 1 and 3. Although the four copper-binding sites were almost identical to those of other multicopper oxidases, the hydrophilic Asn residue (at the same position as a hydrophobic residue such as Leu in other multicopper oxidases) very close to the type I copper might contribute to the characteristically high redox potential of BOD.

Improved magnetic trapped field in thin-wall YBCO single-domain samples by high-pressure oxygen annealing

Oxygen high pressure (up to 16 MPa) has been introduced in the oxygen-annealing step necessary to make the YBa 2Cu 3O x phase superconducting (change x from 6 to about 7). It enables a displacement in the equilibrium phase diagram towards higher temperatures, which means the possibility to achieve the same final oxygen content as the one at low temperature, but with the benefit of higher diffusion rates. Initial development made on thin bars (1.5–3 mm thick) has confirmed the interest of using a high pressure of oxygen. TEM observations have shown an increase of twin density associated with higher Jc. This is in agreement with other works claiming the possibility of higher Jc by twin engineering, and more precisely by twin refinement while annealing at high temperature. We report the successful application of this process without any adjustment to so-called thin-wall single-domain samples. These samples are obtained by growing a crystal on a pellet already shaped with an array of holes. The advantage is that, as far as diffusion processes are concerned, the typical length is not anymore the diameter of the sample, but the thickness of the walls between holes. The trapped field of 16 mm diameter Y123 thin-wall single-domain samples was doubled (0.6 T vs. 0.3 T at 77 K) in a rather short annealing time (about 3 days). Microstructures as well as magneto-optical observations of plain and thin-wall samples evidenced a reduction of cracks in the thin-wall samples. Improved performances were confirmed by further characterizations performed from 77 down to 20 K using the pulse-field facilities of the LNCMP at Toulouse.

不規則性をもつ結晶，超イオン導電体，非晶質，ガラス，融体の構造解析―不規則系・ランダム系の結晶学―１．周期系における不規則性の解析 双晶・ドメイン構造をもつ結晶の解析

Structure refinement method using the data from a twinned crystal is reviewed. For twins whose reciprocal lattices coincide in position, three-dimensional twin operations are used to transform the indices. For twins in which only a part of diffractions from two domains coincide in position, a six-dimensional twin refinement technique is illustrated with a few examples.

Pseudo-merohedrally twinned tetrakis(1H-imidazole-κN3)bis(N-nitrocyanamidato-κN)copper(II)

Crystals of the title complex, [Cu(CN3O2)2(C3H4N2)4], the structure of which has been determined by single-crystal X-ray diffraction at 304 K, appear to be pseudo-merohedrally twinned. Transformation to a monoclinic C-centred cell was necessary in order to derive the twin law. Twin refinement in a triclinic unit cell significantly reduced the R value. The asymmetric unit of the triclinic cell consists of one mol­ecule in a general position and two half entities with the Cu atom on a centre of inversion. The coordination of the Cu atom is quasi-octa­hedral, with four imidazole N-atom donors in the equatorial plane and two cyano N atoms from the N-nitro­cyanamidate anion in axial positions. Owing to symmetry in the centrosymmetric mol­ecules, the trans imidazole ligands are parallel, while those in the non-centrosymmetric mol­ecule make angles of 22.8 (2) and 77.9 (2)°.

Synthesis, Thermal Properties and Crystal Structure of Twinned Crystals of the New Coordination Polymer Poly[(CuBr)2(μ2-pyrimidine-N,N’)

Abstract Reaction of copper(I) bromide with pyrimidine in acetonitrile leads to the formation of crystals of the new coordination polymer poly[(CuBr)2(μ2-pyrimidine-N,N’)]. Indexing of the reflections yields a monoclinic primitive cell with a = 3.9119(2), b = 13.525(1), c = 15.346(1)Å , β = 97.29(1)° and V =805.4(1) Å3. Inspection of the reciprocal space shows weak reflections which might be indicative of a superstructure leading to a doubling of the crystallographic c-axis. The structure can be solved in space group P21/m but the refinement leads to very poor reliability factors (wR2 for all refl.: 62.57%, R1 for all Fo &gt; 4σ (Fo) = 27.84%). A twin refinement assuming merohedral twinning drastically reduces the R-values (wR2 for all refl.: 7.27%, R1 for all Fo &gt; 4σ (Fo) = 2.64%) and a structure model is obtained which consists of two crystallographically independent copper and bromine atoms and two pyrimidine ligands in the asymmetric unit. However, carefull inspection of this structure shows that the two crystallographically independent layers formed by the connection of the building blocks are very similar and that they are related by a translation by half of the crystallographic c-axis. As a result of that, the crystal is just a partial merohedral twin and the reflections which led to the assumption that the c-axis is twice as long are generated by the second twin domain. The structure was refined with the correct twin law (wR2 for all refl.: 6.70%, R1 for all Fo &gt; 4σ (Fo) = 2.57%). By this procedure a reasonable structure model is obtained which consists of one crystallographically independent copper and bromine atom and one pyrimidine ligand. In the crystal structure CuBr double chains are formed which are connected into layers via μ-N,N’ coordination by the N-donor ligands. On heating, the compound loses all of the ligands and transforms into CuBr within only one single step in an exothermic reaction.

A mixed-valence iron complex of the antitumour drug 6-mercaptopurine: tris(6-mercaptopurine)iron(II) tetrachloroferrate(III) chloride.

Single crystals of the title complex, tris(1, 6-dihydro-9H-purine-6-thione-N(7),S)iron(II) tetrachloroferrate(III) chloride, [Fe(C(5)H(4)N(4)S)(3)][FeCl(4)]Cl, were grown on the surface of solid 6-mercaptopurine monohydrate pellets in a solution of iron(III) chloride. The solution of the hexagonal structure required the application of twin refinement techniques. All the component ions lie on threefold rotation axes. The complex contains distorted octahedral [Fe(C(5)H(4)N(4)S)(3)](2+) cations with three N7/S6-chelating neutral 6-mercaptopurine ligands, tetrahedral [FeCl(4)](-) anions with a mean Fe-Cl distance of 2.189 (1) A, and free chloride ions.