A multi-method characterization of natural terrestrial birnessites
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Single crystals of X Pt 5 P (X = Al, Ga, and In), belonging to the 1-5-1 family of compounds, were grown from a Pt-P solution at high temperatures, and measurements of the ambient pressure, temperature-dependent magnetization, resistivity, and x-ray diffraction were made. Additionally, the ambient-pressure Hall resistivity and temperature-dependent resistance under pressure were measured on GaPt 5 P. All three compounds have a tetragonal P4/mmm crystal structure at room temperature with metallic transport and weak diamagnetism over the 2–300 K temperature range. Surprisingly, at ambient pressure, both the transport and magnetization measurements on GaPt 5 P show a steplike feature in the 70–90 K region, suggesting a possible structural phase transition. Neither AlPt 5 P nor InPt 5 P have any signatures of a phase transition in their temperature-dependent electrical resistance and magnetization data. Both the hysteretic nature and sharpness of the features in the GaPt 5 P data suggest that the transition is first-order. Further, single-crystal x-ray diffraction measurements provided further details of the structural transition with a possibility of a crystal symmetry different from P4/mmm below the transition temperature. The transition is characterized by anisotropic changes in the lattice parameters and a volume collapse with respect to the high-temperature tetragonal crystal structure. Furthermore, satellite peaks are observed at two distinct and nonequivalent wave vectors (0, 0, 0.5) and (0.5, 0.5, 0.5), and density functional theory calculations present phonon softening, especially at (0.5, 0.5, 0.5), as a possible driving mechanism. Additionally, we find that the structural transition temperature increases rapidly with increasing pressure, reaching room temperature by ~2.2 GPa, highlighting the high degree of pressure sensitivity of GaPt 5 P and fragile nature of its room-temperature structure. Even though the volume collapse and extreme pressure sensitivity suggest chemical pressure should drive a similar structural change in AlPt 5 P, where both unit-cell dimensions and volume are smaller, its structure is found to be the same as that of the room-temperature GaPt 5 P. Overall, GaPt 5 P stands out as a sole member of the 1-5-1 family of compounds for which a temperature-driven structural change has been observed.
The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB.
The synthesis of new materials is the lifeline of solid-state science, and it continues to offer us unique opportunities for testing various theoretical formulations and models on a practical material. Such an avenue, therefore, provides a breeding ground for technological innovations and advancements that can completely revolutionize our world. Here, we report the results of our exploratory syntheses in the Yb–Cd–Sb compositional space that lead to the identification of two new Zintl antimonides, namely, Yb10CdSb9 and Yb14CdSb11. Their crystal structures were established via single-crystal X-ray diffraction methods; the basic electronic and transport properties of the new materials were also characterized. Yb10CdSb9 crystallizes in a disordered variant of the tetragonal Ca10LiMgSb9 structure type with unit cell parameters a = 11.8473(8) Å and c = 17.1302(12) Å (space group P42/mnm). Yb14CdSb11 crystallizes in the tetragonal Ca14AlSb11 structure type with unit cell parameters: a = 16.605(3) Å and c = 12.144(7) Å (space group I41/acd). Although the structures of both compounds can be rationalized within the framework of the Zintl formalism, based on the partitioning of the valence electrons in the much disordered Yb10CdSb9 phase, the charge is indicative of a slightly electron-rich composition. Electronic structure calculations in both cases support the notion of intrinsic semiconductor behavior, as expected for a Zintl phase. The temperature dependence of the electrical resistivity of a single crystal of Yb10CdSb9 is in line with that, and the evolution of the Seebeck coefficient indicates an electron-dominated transport mechanism, and a respectable power factor of 0.71 μW/cm K2 at 460 K can be calculated for Yb10CdSb9. The electrical resistivity of Yb14CdSb11, however, evolves in a semimetallic manner, which could suggest an overdoped sample or degenerate semiconducting behavior.
Four heteroanionic oxyhalides, CeClMoO 4 , CeBrMoO 4 , CeClWO 4 , and CeBrWO 4 , have been studied as multifunctional materials, which show a combination of good second harmonic generation (SHG) response and photocurrent signals. Millimeter-sized CeHaVIO 4 (Ha = Cl, Br; VI = Mo, W) crystals were grown by halide salt flux. The crystal structure of CeHaVIO 4 crystals was accurately determined by single-crystal X-ray diffraction. CeClMoO 4 , CeBrMoO 4 , and CeBrWO 4 are isostructural to each other, and crystallize in the acentric LaBrMoO 4 structure type. CeClWO 4 crystallizes in a new structure type with unit cell parameters of a = 19.6059(2) Å, b = 5.89450(10) Å, c = 7.80090(10) Å, and β = 101.4746(8)°. The bandgaps of CeHaVIO 4 fall into the range of 2.8(1)–3.1(1) eV, which are much smaller than those of isotypic LaHaVIO 4 (Ha = Cl, Br; VI = Mo, W) in the range of 3.9(1)–4.3(1) eV. The narrowing of bandgaps in CeHaVIO 4 originates from the presence of partially filled 4f orbitals of cerium atoms, which was confirmed by density functional theory (DFT) calculations. The moderate bandgaps make CeHaVIO 4 suitable for infrared nonlinear optical (IR NLO) applications. CeBrMoO 4 and CeBrWO 4 exhibit moderate SHG responses of 0.58× AGS and 0.46× AGS, respectively, and are both type-I phase-matching materials. Moderate SHG response, easy growth of crystals, high ambient stability, and type-I phase-matching behavior make CeBrMoO 4 and CeBrWO 4 great materials for IR NLO applications. CeHaVIO 4 films also exhibited good photocurrent response upon light radiation. Furthermore, this work demonstrates the rich structural chemistry of the REHaVIO 4 (RE = Y, La–Lu; Ha = Cl, Br; VI = Mo, W) family and the potential presence of more multifunctional materials.
Puromycin-sensitive aminopeptidase (E.C. 3.4.11.14, UniProt P55786), a zinc metallopeptidase belonging to the M1 family, degrades a number of bioactive peptides as well as peptides released from the proteasome, including polyglutamine. We report the crystal structure of PSA at 2.3 Å. Overall, the enzyme adopts a V-shaped architecture with four domains characteristic of the M1 family aminopeptidases, but it is in a less compact conformation compared to most M1 enzymes of known structure. A microtubule binding sequence is present in a C-terminal HEAT repeat domain of the enzyme in a position where it might serve to mediate interaction with tubulin. In the catalytic metallopeptidase domain, an elongated active site groove lined with aromatic and hydrophobic residues and a large S1 subsite may play a role in broad substrate recognition. The structure with bound polyglutamine shows a possible interacting mode of this peptide, which is supported by mutation.
Abstract Recently, superconductivity at high temperatures is observed in bulk La 3 Ni 2 O 7−δ under high pressure. However, the attainment of high‐purity La 3 Ni 2 O 7−δ single crystals remains a formidable challenge. Here, the crystal structure and physical properties of single crystals of Sr‐doped La 3 Ni 2 O 7 synthesized at high pressure (20 GPa) and high temperature (1400 °C) are reported. Through single crystal X‐ray diffraction, it is shown that high‐pressure‐synthesized paramagnetic Sr‐doped La 3 Ni 2 O 7 crystallizes in an orthorhombic structure with Ni─O─Ni bond angles of 173.4(2)° out‐of‐plane and 175.0(2)°and 176.7(2)°in plane. The substitution of Sr alters in band filling and the ratio of Ni 2+ /Ni 3+ in Sr‐doped La 3 Ni 2 O 7 , aligning them with those of “La 3 Ni 2 O 7.05” , thereby leading to significant modifications in properties under high pressure relative to the unsubstituted parent phase. At ambient pressure, Sr‐doped La 3 Ni 2 O 7 exhibits insulating properties, and the conductivity increases as pressure goes up to 10 GPa. However, upon further increasing pressure beyond 10.7 GPa, Sr‐doped La 3 Ni 2 O 7 transits back from a metal‐like behavior to an insulator. The insulator–metal–insulator trend under high pressure dramatically differs from the behavior of the parent compound La 3 Ni 2 O 7−δ , despite their similar behavior in the low‐pressure regime. These experimental results underscore the considerable challenge in achieving superconductivity in nickelates.
Metal silicon phosphides composed of earth-abundant Si and P tend to exhibit semiconducting properties and adopt diverse crystal structures with relatively small additions of structure-directing elements. The potential of silicon phosphide materials in nonlinear optical applications has been hindered by the inability to systematically produce noncentrosymmetric structures with such a flexible framework. Here, in this work, two isostructural compounds with a novel noncentrosymmetric structure were made possible by the inclusion of elements with stereochemically active lone pairs (Sn 2+ and Pb 2+ ). The structures were determined through single-crystal and synchrotron powder X-ray diffraction. Analysis of chemical bonding in real space through the electron localization function revealed stereochemically active Pb 2+ and Sn 2+ species in a trigonal pyramidal coordination with {Pb/Sn}–P bonds. Such covalent bonding between Pb and P is quite uncommon in extended solids and has been reported in a few rare instances. Band structure calculations and linear optical measurements confirm the semiconducting nature of Cs X Si 15 P 21 ( X = Sn or Pb). The synthesis was optimized to yield high-purity polycrystalline samples. The nonlinear optical properties show promising second-harmonic generation (SHG) coefficients from the Kurtz–Perry method. First-principles calculations of the nonlinear optical properties support the experimentally determined SHG values and provide moderate values of birefringence, suggesting Cs X Si 15 P 21 could be phase-matchable and practical nonlinear optical materials in the mid-IR region.
Abstract The niobium oxide polymorph T -Nb 2 O 5 has been extensively investigated in its bulk form especially for applications in fast-charging batteries and electrochemical (pseudo)capacitors. Its crystal structure, which has two-dimensional (2D) layers with very low steric hindrance, allows for fast Li-ion migration. However, since its discovery in 1941, the growth of single-crystalline thin films and its electronic applications have not yet been realized, probably due to its large orthorhombic unit cell along with the existence of many polymorphs. Here we demonstrate the epitaxial growth of single-crystalline T -Nb 2 O 5 thin films, critically with the ionic transport channels oriented perpendicular to the film’s surface. These vertical 2D channels enable fast Li-ion migration, which we show gives rise to a colossal insulator–metal transition, where the resistivity drops by 11 orders of magnitude due to the population of the initially empty Nb 4 d 0 states by electrons. Moreover, we reveal multiple unexplored phase transitions with distinct crystal and electronic structures over a wide range of Li-ion concentrations by comprehensive in situ experiments and theoretical calculations, which allow for the reversible and repeatable manipulation of these phases and their distinct electronic properties. This work paves the way for the exploration of novel thin films with ionic channels and their potential applications.
Metal organic frameworks (MOFs) are porous crystalline materials that display a wide variety of physical and chemical properties. Their single crystal structure determination is often challenging because in most cases micro- or nano-sized crystals spontaneously form upon MOF synthesis, which cannot be recrystallized. The production of larger single crystals for structure determination involves optimizing, and thus modifying, the conditions of synthesis, in which success cannot be guaranteed. Failure to produce crystals suitable for single-crystal X-ray diffraction leaves the 3D structure of the MOF compound unknown, and scientists must resort to more challenging structure solution methods based on X-ray powder or electron diffraction data. These laborious tasks can be avoided by using serial crystallography techniques which merge data collected on many micro-crystals. Here, we report the application of three synchrotron serial crystallography methods. We call these “mesh”, “grid” and “mesh&collect” scans. “Still” images (no rotation) are collected in the mesh scan approach, whereas small rotational wedges are collected in the grid scan method. The third protocol, mesh&collect, combines the acquisition of still images and rotational wedges. Using these means, we determine the ab initio structure of benchmark MOFs, MIL-100(Fe) and ZIF-8, that differ largely in unit cell size. These methods are expected to be widely applicable and facilitate structure determination of many MOF microcrystalline systems.
The endonuclease Artemis is responsible for opening DNA hairpins during V(D)J recombination and for processing a subset of pathological DNA double-strand breaks. Artemis is an attractive target for the development of therapeutics to manage various B cell and T cell tumors, because failure to open DNA hairpins and accumulation of chromosomal breaks may reduce the proliferation and viability of pre-T and pre-B cell derivatives. However, structure-based drug discovery of specific Artemis inhibitors has been hampered by a lack of crystal structures. Here, we report the structure of the catalytic domain of recombinant human Artemis. The catalytic domain displayed a polypeptide fold similar overall to those of other members in the DNA cross-link repair gene SNM1 family and in mRNA 3'-end-processing endonuclease CPSF-73, containing metallo-β-lactamase and β-CASP domains and a cluster of conserved histidine and aspartate residues capable of binding two metal atoms in the catalytic site. As in SNM1A, only one zinc ion was located in the Artemis active site. However, Artemis displayed several unique features. Unlike in other members of this enzyme class, a second zinc ion was present in the β-CASP domain that leads to structural reorientation of the putative DNA-binding surface and extends the substrate-binding pocket to a new pocket, pocket III. Moreover, the substrate-binding surface exhibited a dominant and extensive positive charge distribution compared with that in the structures of SNM1A and SNM1B, presumably because of the structurally distinct DNA substrate of Artemis. The structural features identified here may provide opportunities for designing selective Artemis inhibitors.
Tuning the crystal phase of bimetallic nanocrystals offers an alternative avenue to improving their electrocatalytic performance. Herein, we present a facile and one-pot synthesis approach that is used to enhance the catalytic activity and stability toward oxygen reduction reaction (ORR) in alkaline media via control of the crystal structure of Pd-Bi nanocrystals. By merely altering the types of Pd precursors under the same conditions, the monoclinic structured Pd 5 Bi 2 and conventional face-centered cubic (fcc) structured Pd 3 Bi nanocrystals with comparable size and morphology can be precisely synthesized, respectively. Interestingly, the carbon-supported monoclinic Pd 5 Bi 2 nanocrystals exhibit superior ORR activity in alkaline media, delivering a mass activity (MA) as high as 2.05 A/mg Pd . After 10,000 cycles of ORR durability test, the monoclinic structured Pd 5 Bi 2 /C nanocatalysts still remain a MA of 1.52 A/mg Pd , which is 3.6 times, 16.9 times, and 21.7 times as high as those of the fcc Pd 3 Bi/C counterpart, commercial Pd/C, and Pt/C electrocatalysts, respectively. Moreover, structural characterizations of the monoclinic Pd 5 Bi 2 /C nanocrystals after the durability test demonstrate the excellent retention of the original size, morphology, composition, and crystal phase, greatly alleviating the leaching of the Bi component. Overall, this work provides new insight for the synthesis of multimetallic catalysts with a metastable phase and demonstrates phase-dependent catalytic performance.
The crystal structure of the [Co(NH 3 ) 6 ] 2 [ReF 6 ] 3 ·3H 2 O (I) salt is reported. The salt crystallizes in the trigonal space group P31m with the following unit cell dimensions: a = 15.8714(4) Å, b = 15.8714(4) Å, and c = 9.8657(4) Å. Here, the structure of (I) consists of [Co(NH 3 ) 6 ] 3+ cations, [ReF 6 ] 2– anions, and co-crystallized water molecules which are linked by hydrogen bonding. In (I), independent [ReF 6 ] 2– anions and [Co(NH 3 ) 6 ] 3+ cations octahedron are slightly distorted. Characteristic vibration bands of the [Co(NH 3 ) 6 ] 3+ cation, [ReF 6 ] 2– anion as well as the co-crystallized H 2 O molecules are observed in the infrared spectra of (I). UV-Visible analyses in water showed that the absorption of the [Co(NH 3 ) 6 ] 3+ cation predominate the spectra of (I).
SO 2 linkage photoisomerization in crystalline ruthenium-based complexes has demonstrated nanophotonic phenomena such as optical switching and nano-optomechanical transduction. Molecular insights into these materials have been explored largely via the characterization of their photoinduced crystal structures via in situ single-crystal X-ray diffraction, known as photocrystallography. Photoinduced molecular disorder is present, which photocrystallography can model to the extent that it is confined within the periodic boundary of a unit cell. However, non-periodic molecular disorder is suspected to exist as well. In situ total scattering experiments were therefore carried out on finely powdered crystals of four ruthenium-sulfur dioxide complexes. Data were modeled using light-minus-dark' difference pair distribution function analysis, which afforded photoinduced structural changes exclusively. This revealed structural features that were first compared against models of photoinduced crystal structures known a priori from photocrystallography. Furthermore, statistical inference was then employed, which evidenced generally good agreement between the total scattering data and the photocrystallographic models, while revealing real differences that are indicative of a structure with only a short-range order. Overall, our findings demonstrate that in situ light-induced total scattering experiments on finely powdered crystals are able to reveal the photoinduced structure. Overall, the evidence suggests that such structure could include a short-range order as well as photocrystallographic content. Our demonstration experiment offers a pathway to develop studies that capture the short-range order in linkage photoisomers, while we have outlined the procedure for testing the validity of associated structural models.
Bruton’s tyrosine kinase (BTK) is the target of the therapeutic agent, Ibrutinib, that treats chronic lymphocyte leukemia (CLL), mantle cell lymphoma (MCL) and other B cell malignancies. Ibrutinib is a first in class, covalent BTK inhibitor that limits B-cell survival and proliferation. Designing new inhibitors of BTK has been an important objective for advancing development of improved therapeutic agents against cancer and autoimmune disorders. Based on the success of Ibrutinib, several second-generation irreversible BTK inhibitors have been developed that exhibit fewer off-target effects. However, the binding-mode and their interaction with Btk have not been experimentally determined and evaluated at atomic resolution. Here we determined the first crystal structure of the BTK kinase domain in complex with acalabrutinib. In addition, we report a structure of the BTK/tirabrutinib complex and compare these structures with previously solved structures. The structures provide insight in the superior selectivity reported for acalabrutinb and guide future BTK inhibitor development.
Recently, hybrid organic−inorganic copper(I) metal halides have attracted global attention due to their intriguing optical properties and low-cost solution processability. In this work, we report three hybrid organic−inorganic copper(I) bromides, [TMPA] 2 [Cu 2 Br 4 ], [TMPA] 4 [Cu 6 Br 10 ], and [TMPA] 2 [Cu 4 Br 6 ], synthesized through a slow evaporation method using trimethylphenylammonium (TMPA + ) as the organic cation. By precise control of the CuBr and TMPABr precursors, different copper halide [Cu 2 Br 4 ] 2− , [Cu 6 Br 10 ] 4− , and [Cu 4 Br 6 ] 2− structural units can be obtained. [TMPA] 2 [Cu 2 Br 4 ], [TMPA] 4 [Cu 6 Br 10 ], and [TMPA] 2 [Cu 4 Br 6 ] demonstrate distinct blue, orange, and greenish-yellow light emission, respectively. The first two compounds have zero-dimensional (0D) crystal structures in centrosymmetric triclinic space group P-1 and monoclinic space group P2 1 /n. In contrast, [TMPA] 2 [Cu 4 Br 6 ] features a unique one-dimensional (1D) structure and crystallizes in the centrosymmetric monoclinic space group P2 1 /c. Consequently, the observed greenish-yellow emission of [TMPA] 2 [Cu 4 Br 6 ] is also unique, in contrast to the typical orange-red emission of 0D [Cu 4 Br 6 ]-based compounds. This work provides insights into the design of copper halide light emitters and emphasizes the influence of structural dimensionality on photoluminescence. The tunable optical properties suggest the potential of these materials for multicolor photopatterning, information encryption, and anticounterfeiting applications.
Here we report the effect of alkyl side chain branching on melt-recrystallization of nanoconfined polypeptoid films using poly(N-octyl glycine) (PNOG) and poly(N-2-ethyl-1-hexyl glycine) (PNEHG) as model systems. Upon cooling from the isotropic melt, confined PNOG molecules recrystallize into a near-perfect orthorhombic crystal structure with the board-like molecules stacked face-to-face in the substrate-parallel direction, resulting in long-range ordered wormlike lamellae that occupy the entire film. By contrast, rod-like PNEHG molecules bearing branched N-2-ethyl-1-hexyl side chains stack into a columnar hexagonal mesophase with their backbones oriented parallel to the substrates, forming micron-sized sheaf-like superstructures under confinement, exposing large areas of empty spaces in the film. These findings highlight the effect of alkyl side chain branching on the packing motif and multiscale crystalline structure of polypeptoids under a nanoconfined geometry.
Two-dimensional (2D) tin halide perovskites are highly tunable and low-toxicity semiconductors, promising for next-generation optoelectronics. However, achieving air stability and excellent photophysical properties simultaneously necessitates deliberate structure tuning using organic spacer cations and A-site cations. Here, we report a series of new quasi-2D Ruddlesden–Popper tin halide perovskites using a fluorinated aromatic spacer cation, 4-fluorophenethylammonium (4FPEA), and systematically investigate the impacts of layer thickness, spacer cation, and A-site cation on the crystal structures and optical properties of (4FPEA) 2 (A) n−1 S n I 3n+1 . These 4FPEA-based 2D tin perovskites, further tuned by the A-cations, exhibit uniquely undistorted 180° out-of-plane Sn–I–Sn bond angles and low octahedral distortions compared to other quasi-2D perovskites and demonstrate prolonged air stability, excellent photophysics, and amplified spontaneous emission and lasing in exfoliated microflakes. A comprehensive survey of reported n = 2 lead and tin iodide perovskites reveals that all structures can be classified into three types (tilted, balanced, and buckled) based on the structural distortion parameters of their perovskite cages. Notably, (4FPEA) 2 (A)Sn 2 I 7 are among the handful of “balanced” n = 2 perovskites with minimal distortion and excellent optoelectronic performance. Furthermore, the structural insights and cage-balancing approach revealed herein motivate the deliberate design of quasi-2D perovskites through the synergy of the spacer and cage cations, further paving the way for high-performance optoelectronic applications of stable tin halide perovskites.