Higher Symmetry Space Group Research Articles

Mechanism of Negative Thermal Expansion in Monoclinic Cu2P2O7 from First Principles.

Negative thermal expansion (NTE) materials generally have high-symmetry space groups, large average atomic volumes, and corner-sharing octahedral and tetrahedral coordination structures. By contrast, monoclinic α-Cu2P2O7, which has a small average atomic volume and edge-sharing structure, has been reported to exhibit NTE, the detailed mechanism of which is unclear. In this study, we investigate the A2B2O7 polymorphs and analyze the NTE behavior of α-Cu2P2O7 using first-principles lattice-dynamics calculations. From the polymorphism investigation in 20 A2B2O7 compounds using 6 representative crystal structures, small A and B cationic radii are found to stabilize the α-Cu2P2O7-type structure. We then analyze the NTE behavior of α-Cu2P2O7 using quasi-harmonic approximation. Our calculated thermal expansion coefficients and anisotropic atomic displacement parameters were in good agreement with those of the experimental reports at low temperatures. From the mode-Grüneisen parameter distribution plotted over the entire first-Brillouin zone, we found that the phonon contributing most significantly to NTE emerges not into the special points but between them. In this phonon mode, the O connecting two PO4 tetrahedra rotates, and the Cu and O vibrate perpendicular to the bottom of the CuO5 pyramidal unit, which folds the ac lattice plane. This vibration behavior can explain the experimentally reported anisotropic NTE behavior of α-Cu2P2O7. Our results demonstrate that the most negative mode-Grüneisen parameter contributing to NTE behavior is not always located on high-symmetry special points, indicating the importance of lattice vibration analyses for the entire first-Brillouin zone.

High-resolution crystal structure of the Mu8.1 conotoxin from Conus mucronatus.

Marine cone snails produce a wealth of peptide toxins (conotoxins) that bind their molecular targets with high selectivity and potency. Therefore, conotoxins constitute valuable biomolecular tools with a variety of biomedical purposes. The Mu8.1 conotoxin from Conus mucronatus is the founding member of the newly identified saposin-like conotoxin class of conotoxins and has been shown to target Cav2.3, a voltage-gated calcium channel. Two crystal structures have recently been determined of Mu8.1 at 2.3 and 2.1 Å resolution. Here, a high-resolution crystal structure of Mu8.1 was determined at 1.67 Å resolution in the high-symmetry space group I4122. The asymmetric unit contained one molecule, with a symmetry-related molecule generating a dimer equivalent to that observed in the two previously determined structures. The high resolution allows a detailed atomic analysis of a water-filled cavity buried at the dimer interface, revealing a tightly coordinated network of waters that shield a lysine residue (Lys55) with a predicted unusually low side-chain pKa value. These findings are discussed in terms of a potential functional role of Lys55 in target interaction.

The curious case of the structural phase transition in SnSe insights from neutron total scattering

At elevated temperatures SnSe is reported to undergo a structural transition from the low symmetry orthorhombic GeS-type to a higher symmetry orthorhombic TlI-type. Although increasing symmetry should likewise increase lattice thermal conductivity, many experiments on single crystals and polycrystalline materials indicate that this is not the case. Here we present temperature dependent analysis of time-of-flight (TOF) neutron total scattering data in combination with theoretical modeling to probe the local to long-range evolution of the structure. We report that while SnSe is well characterized on average within the high symmetry space group above the transition, over length scales of a few unit cells SnSe remains better characterized in the low symmetry GeS-type space group. Our finding from robust modeling provides further insight into the curious case of a dynamic order-disorder phase transition in SnSe, a model consistent with the soft-phonon picture of the high thermoelectric power above the phase transition.

Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi.

The utility of X-ray crystal structures determined under ambient-temperature conditions is becoming increasingly recognized. Such experiments can allow protein dynamics to be characterized and are particularly well suited to challenging protein targets that may form fragile crystals that are difficult to cryo-cool. Room-temperature data collection also enables time-resolved experiments. In contrast to the high-throughput highly automated pipelines for determination of structures at cryogenic temperatures widely available at synchrotron beamlines, room-temperature methodology is less mature. Here, the current status of the fully automated ambient-temperature beamline VMXi at Diamond Light Source is described, and a highly efficient pipeline from protein sample to final multi-crystal data analysis and structure determination is shown. The capability of the pipeline is illustrated using a range of user case studies representing different challenges, and from high and lower symmetry space groups and varied crystal sizes. It is also demonstrated that very rapid structure determination from crystals in situ within crystallization plates is now routine with minimal user intervention.

Cyclo-hexane plastic phase I: single-crystal diffraction images and new structural model.

The plastic phase of cyclohexane (polymorph I) was studied by Kahn and co-workers, without achieving a satisfactory determination of the atomic coord-inates [Kahn et al. (1973). Acta Cryst. B29, 131-138]. The positions of the C atoms cannot be determined directly as a consequence of the disorder in a high-symmetry space group, an inherent feature of plastic materials. Given this situation, the building of a polyhedron describing the disorder was the main tool for determining the molecular structure in the present work. Based on the shape of reflections {111}, {200} and {113} in space group Fm 3 m, we assumed that cyclohexane is disordered through the action of rotation group 432. The polyhedral cluster of disordered molecules is then a rhombic dodecahedron centred on the nodes of an fcc Bravais lattice. The vertices of this polyhedron are the positions of C atoms for the cyclohexane molecule, which is disordered over 24 positions. With such a model, the asymmetric unit is reduced to two C atoms placed on special positions, and an acceptable fit between the observed and calculated structure factors is obtained.

Synthesis, Crystal Packing Aspects and Pseudosymmetry in Coordination Compounds with a Phosphorylamide Ligand

This work reports the synthesis and crystal structure of new closely related coordination compounds, [ML2]·nTHF, where M is Zn or Mn; L is a phosphorylmethylamide derivative of benzothiadiazole; n = 1 (M = Zn) and 1, 2 (M = Mn); and THF is tetrahydrofuran. The zinc compound, 1·THF, crystallizes in a high-symmetry space group, I41/a, that is relatively rare for compounds with organic ligands. The corresponding manganese congener, 2·THF, with a similar crystal packing, features a pseudosymmetrical structure P21/c of the doubled volume of the unit cell as compared to 1·THF. The main difference between the structures lies in a different arrangement of solvate THF molecules, which likely modulates the crystal packing of the complexes. Another manganese solvatomorph, 2·2THF, reveals a fundamentally different crystal packing while exhibiting a similar geometry of the complex. We consider the problem of localization of solvate THF molecules and the types of their disorder by the example of compounds 1–2.

Organic–Inorganic Hybrid Compound [H2-1,5-Diazabicyclo[3.3.0]octane]ZnBr4 with Reverse Symmetry Breaking Shows a Switchable Dielectric Anomaly and Robust Second Harmonic Generation Effect

An organic-inorganic hybrid molecule [3.3.0-H2dabco]ZnBr4 (1) with switchable phase transition, dielectric anomaly, and second harmonic generation (SHG) effect was synthesized by reaction of 1,5-diazabicyclo[3.3.0]octane (3.3.0-dabco) with ZnBr2 in concentrated hydrobromic acid aqueous solution. Differential scanning calorimetry (DSC) and dielectric measurements revealed that 1 exhibits a reversible high-temperature phase transition, accompanied by a distinct step-like dielectric anomaly at 373 K. Exceptionally, the single crystal structure analysis at different temperatures revealed that 1 undergoes reverse symmetry breaking during the phase transition, in which the high-symmetry space group Cc in the low temperature phase (LTP) is transformed to the low-symmetry space group P1̅ in the high temperature phase (HTP). In addition, with the conversion from the non-centrosymmetric (NCS) to the centrosymmetric (CS) space group, the SHG of 1 can switch from SHG-ON to SHG-OFF for at least four cycles without obvious decay.

UoC-6: a first MOF based on a perfluorinated trimesate ligand

Abstract Reaction of Sc(NO3)3·5H2O with K(H2 pF-BTC) – the monopotassium salt of perfluorinated trimesic acid – led to the formation of single crystals of [ Sc ( p F − BTC ) ( H 2 O ) 3 ] ∞ 1 ⋅ 4 H 2 O ${}_{\infty }{}^{1}\left[\text{Sc}\left(pF-\text{BTC}\right){\left({\text{H}}_{2}\text{O}\right)}_{3}\right]\cdot 4{\text{H}}_{2}\text{O}$ ( P 1 ‾ $P‾{1}$ , Z = 2). DTA/TGA measurements revealed that all water molecules were released below 200 °C. Using powder synchrotron radiation diffraction data, the crystal structure of the residue of the dehydration was elucidated and the results confirmed the formula [ Sc ( p F − BTC ) ] ∞ 3 ${}_{\infty }{}^{3}\left[\text{Sc}\left(pF-\text{BTC}\right)\right]$ (Fddd, Z = 16). The compound is similar, but not isostructural to the recently published UoC-4 (I41/amd, Z = 8; UoC: University of Cologne) with a difluorinated trimesate (dF-BTC3–) as connecting linker. Both compounds can be classified as metal-organic frameworks (MOFs) consisting of a 3D network of Sc3+ nodes connected by the fluorinated trimesate ligands. They contain small pores, but their opening windows are too small for any guest molecules to pass. Remarkably, UoC-4 with a lower symmetric ligand (dF-BTC3–) crystallizes in a higher symmetry space group (I41/amd) than UoC-6 (Fddd). This can be rationalized by increasing torsion angles of the carboxylate moieties in the pF-BTC3– ligand.

Synthesis and crystal structures of novel alkali rare-earth orthoborates K3RE3(BO3)4 (RE = Pr, Nd, Sm–Lu)

We report a series of novel alkali rare-earth orthoborates K3RE3(BO3)4 (RE = Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb and Lu) prepared by high-temperature solid-state syntheses. Single crystals of K3Pr3(BO3)4, K3Er3(BO3)4, K3Tm3(BO3)4, K3Yb3(BO3)4 and K3Lu3(BO3)4 are obtained by spontaneous crystallization using a flux. Complementary single-crystal and powder X-ray diffraction measurements followed by structure refinements reveal that both Pr- and Nd-containing phases crystallize in the space group P $$\overline{1}$$ (Z = 4), whereas the other K3RE3(BO3)4 members with higher atomic number (RE = Sm–Lu) crystallize in the higher symmetry space group P21/c (Z = 8). Amid differences in the space groups, each member of the series keeps close structural correlations in their motif and connectivity. The crystal structures of K3RE3(BO3)4 (RE = Sm–Lu) consist of quasi-two-dimensional [RE8(BO3)8] layers parallel to the ab-plane which are connected by out-of-layer RE2O12 and RE2O14 dimers as well as BO3 groups in the c-direction, forming a 3D framework. On the other hand, both K3Pr3(BO3)4 and K3Nd3(BO3)4 phases are comprised of the [RE4(BO3)4] layers, indicating the absence of 21 screw axis along the b-axis. The K+ cations are located between the [RE8(BO3)8] and [RE4(BO3)4] layers, occupying the interstitial voids. All samples exhibit characteristic absorption features in the UV/Vis range relevant to the rare-earth cations, and their optical band gaps are evaluated by both conventional Tauc plot and derivation of absorption spectrum fitting (DASF) methods. The geometric deviations away from the D3h symmetry of the BO3 planar groups are verified using Fourier transformed infrared and Raman spectra, and supported by the X-ray diffraction results.

Hexagonal and monoclinic NaNi0.8Co0.15Al0.05O2 (Na-NCA) for sodium ion batteries

Sodium-ion batteries have emerged as a potential alternate battery chemistry to lithium ion batteries. In this paper, NaNi0.8Co0.15Al0.05O2 (Na-NCA) materials with hexagonal O3 or monoclinic O′3 structure were synthesized by either quenching or slow cooling after heating the precursors. Oxygen vacancies present during the cooling process were found to be the reason for structural differences. Quenched O3-type material has a lower concentration of Jahn-Teller active Ni3+, leading to the formation of high symmetry space group R3¯m. Both materials show better electrochemical performance than NaNiO2. In situ and Ex situ XRD were used to study the structure transitions of both materials during cycling. The structure change during cycling was found to be more reversible for quenched O3-type materials. It is anticipated that this study offers a new strategy for the development of sodium ion battery cathode materials.

Cage-like salt with N-N single bonds

All-nitrogen salts have attracted much attention because of their potential applications as high-energy density materials for explosive or propulsion. Here, we design a cage-like salt Be3N10 with pure N-N single bonds via releasing the pressure of the cage-like diamondoid “N10”, high-pressure phase of nitrogen, and introducing beryllium atoms to stabilize the crystal. At ambient conditions, Be3N10 comprises two anions and six Be2+ cations in a unit cell with high space symmetry (space group ). The Be3N10 salt is kinetically and thermodynamically stable with a 3.06 eV band gap at 0 GPa and room temperature. Further analysis of the chemical bonding pattern and electronic properties reveals that the introduced Be atoms contribute electrons to passivate the dangling bonds of the N10 cluster, and stabilize the system through both Coulomb interactions and covalent bonds. The outstanding properties, including high-energy density (5.75 kJ/g), high nitrogen content (83.8%), and high dynamical stability, make Be3N10 a promising high-energy density material. Our work represents a significant step toward the all-nitrogen salt with pure N-N single bonds.

Crystal Structures and Electronic Properties of Oxygen-rich Titanium Oxides at High Pressure

Pressure is well-known to significantly change the bonding patterns of materials and lift the reactivity of elements, leading to the synthesis of unconventional compounds with fascinating properties. Titanium-oxygen (Ti-O) compounds (e.g., TiO2) are attracting increasing attention due to their attractive electronic properties and extensive industrial applications (e.g., photocatalysis and solar cells). Using the effective CALYPSO structure searching method combined with first-principles calculations, we theoretically explored various oxygen-rich Ti-O compounds at pressures ranging from 0 to 200 GPa. Our results revealed, unexpectedly, that pressure stabilizes two hitherto unknown stoichiometric oxygen-rich Ti2O5 and TiO3 compounds. Ti2O5 crystallized in P-421 c structure, whose remarkable feature is that it contains a peroxide group (O22-) with an O-O distance of 1.38 Å at 150 GPa. The trioxide TiO3 is an ionic metal and is the oxygen-richest compound known thus far in the Ti-O system. It adopts a high symmetry (space group Pm-3 n) structure consisting of a 12-fold coordinated face-sharing TiO12 icosahedron, where Ti has the highest coordination number with O among all Ti-O structures. The underlying mechanisms for the stabilization of Ti2O5 and TiO3 lie in the higher coordination number and denser structure packing. Our current results unravel the unusual oxygen-rich stoichiometry of Ti-O compounds and provide further insight into the diverse electronic properties of Ti oxides under high pressure.

Ibrutinib Polymorphs: Crystallographic Study

In this paper, we present a comprehensive crystallographic study of Ibrutinib polymorphs and their behavior. Three neat polymorphs (A, B, and C) and a methanol solvate (F) were obtained and characterized. The structures of forms A, C, and F were solved from single-crystal diffraction data. Form B has only ever been prepared as a powder, and its structure solution has, so far, not been successful. Polymorph C is a desolvate of the methanol solvate F, and its structure was solved via the single-crystal to single-crystal transformation. The analysis of the solved structures revealed significant differences in the crystal packing of form A in comparison with the previously described Ibrutinib structures, enabling it to crystallize in a higher symmetry space group (monoclinic vs triclinic). The structures also revealed a high similarity between forms C and F, explaining their mutual transformability. To further analyze the solids, we performed DSC, long-term slurry transformations, intrinsic dissolution experi...

The Importance of Polymorphism in Metal-Organic Framework Studies.

Polymorphic phase transitions remain frequently undetected in routine metal-organic framework (MOF) studies; however, their discovery is of major importance in interpreting structure-property relationships. We herein report a reversible enantiotropic single-crystal to single-crystal polymorphic phase transition of a new microporous MOF [Eu(BDC)(NO3)(DMF)2]n (H2BDC = 1,4-benzenedicarboxylic acid; DMF = dimethylformamide). While modification 1LT at 170 K crystallizes in the monoclinic space group P21/c with unit cell dimensions of a = 17.673(2) Å, b = 20.023(2) Å, c = 10.555(9) Å, β = 90.129(4)°, modification 1HT at 290 K crystallizes in higher symmetry space group C2/c with unit cell dimensions of a = 17.200(7) Å, b = 10.737(4) Å, c = 10.684(4) Å, β = 90.136(2)°. This temperature-induced phase transition is accompanied by a small change in the solvent-accessible voids from 46.8 in 1LT to 49.8% in 1HT, which triggers a significant change in the adsorption properties as compared to a reported isostructural compound. Detailed investigations on the phase transition were studied with variable-temperature single-crystal X-ray diffraction (SCXRD), powder X-ray diffraction, and differential scanning calorimetry measurements. The herein-presented investigations emphasize the importance of polymorphic phase transitions in routine MOF studies originating from low-temperature SCXRD data and high-temperature physical property characterizations in avoiding the use of a wrong structure in interpreting structure-property relationships.

Semiconductors and Aperiodic Structures in Organocyanide-Based Materials

Organocyanides such as TCNQ (tetracyanoquinodimethane) and DCNQI (dicyanoquinodiimine) are excellent electron acceptors and have been extensively studied in electrically conducting/switching and magnetic materials. Supramolecular interactions such as π-stacking and hydrogen bonding in addition to coordination bonds with metal ions play an important role in the self-assembly of these functional inorganic materials. A novel semiconductor Cd2(TCNQ)3.5(H2O)2 with non-integer valences of TCNQ was synthesized and is the first example that exhibits four bridging modes of TCNQ in one structure (Figure 1). Despite the rather large stacking distance of 3.687(1) Å between the two μ3-TCNQ species, which constitute a "broken link" in the electron conducting pathway, the semiconductor exhibits a room temperature conductivity of 5.8×10-3 S·cm-1. The hydrogen bonding interactions between the coordinated water molecules and nitrogen atoms of the mu2- and mu3-TCNQ help to stabilize these coordinatively unsaturated TCNQ species. Another application of the chemistry of organocyanides in the context of this research is the study of reactions of the meta-dicyanamidobenzene dianion (DCYD2-) which was predicted by Ruiz and coworkers to facilitate ferromagnetic interactions between certain paramagnetic metal ions. The DCYD2- anion self-assembles with Mn(II) building blocks to afford a rare example of inorganic quadruple helices with an incommensurate modulated structure (Figure 2a). A supercell in the high symmetry space group P4/nnc is obtained with a c parameter five times that of the basic structure and a further 15-fold expansion in the space group of P1 along the c axis reveals that ~2% of Mn positions are disordered. The packing of these helical chains through π-stacking of pyridyl groups leads to 1D nanochannels with an estimated empty volume of 38.6% of the super cell volume (31,587Å3). However, in the presence of water, hydrogen bonding between the water molecules and the cyano-N atoms dominates and only zig-zag chains are formed (Figure 2b).

Partial rotational lattice order–disorder in stefin B crystals

At present, the determination of crystal structures from data that have been acquired from twinned crystals is routine; however, with the increasing number of crystal structures additional crystal lattice disorders are being discovered. Here, a previously undescribed partial rotational order-disorder that has been observed in crystals of stefin B is described. The diffraction images revealed normal diffraction patterns that result from a regular crystal lattice. The data could be processed in space groups I4 and I422, yet one crystal exhibited a notable rejection rate in the higher symmetry space group. An explanation for this behaviour was found once the crystal structures had been solved and refined and the electron-density maps had been inspected. The lattice of stefin B crystals is composed of five tetramer layers: four well ordered layers which are followed by an additional layer of alternatively placed tetramers. The presence of alternative positions was revealed by the inspection of electron-density score maps. The well ordered layers correspond to the crystal symmetry of space group I422. In addition, the positions of the molecules in the additional layer are related by twofold rotational axes which correspond to space group I422; however, these molecules lie on the twofold axis and can only be related in a statistical manner. When the occupancies of alternate positions and overlapping are equal, the crystal lattice indeed fulfills the criteria of space group I422; when these occupancies are not equal, the lattice only fulfills the criteria of space group I4.

Chapter Eight - Crystallization and X-ray Structure Determination of an RNA-Dependent Hexameric Helicase

Hexameric helicases couple the energy of ATP hydrolysis to processive movement along nucleic acids and are critical components of cells and many viruses. Molecular motion derives from ATP hydrolysis at up to six distinct catalytic centers, which is coupled to the coordinated action of translocation loops in the center of the hexamer. Due to the structural dynamics and catalytic complexity of hexameric helicases, few have been crystallized with a full complement of bound substrates, and instead tend to form crystals belonging to high-symmetry space groups that obscure the differences among catalytic subunits. We were able to overcome these difficulties and solve an asymmetric structure of the Rho transcription termination factor from Escherichia coli bound to ATP mimics and RNA. Here, we present some considerations used for crystallization of this hexameric helicase, discuss the utility of substrate-centric crystal-screening strategies, and outline a crystal-aging screen that allowed us to overcome the adverse effects of nonmerohedral twinning.

Chiral and Porous Coordination Polymers Based on an N-Centered Triangular Rigid Ligand

Four cadmium and cobalt coordination polymers with unique structures and topologies have been successfully synthesized under solvothermal conditions by employing an elongated triangular rigid N-containing ligand tris(4-(1H-imidazol-1-yl)phenyl)amine (TIPA) and 5-hydroxyisophthalic acid (5-OH-H2bdc) as anion coligand. Compounds 1−4 were characterized by single crystal X-ray structure analyses, thermogravimetric analyses, SHG, and photoluminescent measurements. Compound 1 crystallizes in the chiral space group C2 (No. 5) and features a 2D → 3D parallel/parallel inclined polycatenated framework. Compound 2 crystallizes in trigonal symmetry with a high-symmetry space group R3 and features a 2D porous noninterpenetrating coordination network. Compound 3 crystallizes in the monoclinic space group P21/n and shows a 2D → 3D parallel/parallel polycatenation framework, and compound 4 crystallizes in the orthorhombic chiral space group P212121 (No. 19) and shows a very rarely 3D + 3D heterogeneous 2-fold interpenet...

Centrosymmetric cyananilic acid: a molecule for functional solids

This article investigates the recent research on a series of anilic acid molecules. The crystallisation of molecules in high symmetry space groups is discussed and rationalised by the arrangement of charge-transfer complexes, which leads to the occurrence of repeated embrace motifs. Since 1997, cyananilic acid (2,5-dicyano-3,6-dihydroxy-1,4-benzoquinone) has been explored due to its valuable physico-chemical features. It is an organic acid that has Mott-insulator properties and organic ferroelectricity. Understanding these properties is an active area of supramolecular chemistry.

ChemInform Abstract: The [Cu8Br15]6- Ion, a Crystal-Stabilized High-Symmetry Mixed-Valence Copper Complex with a Linear Halogen Bridge.

The [Cu8Br15]6- ion in green crystalline (MePh3P)6[Cu8Br15] is shown by X-ray crystallography to have the structure [Br3(μ3-Br4Cu4)(μ2-Br)(μ3-Br4Cu4)Br3]6- derived from two Cu4Br8 cubane units. The unusual geometry and charge of the anion are determined by the high-symmetry (space group Pa3) lattice of cations, maintained by phenyl···phenyl interactions, and interacting with the anion by C−H···Br hydrogen bonds.