Crystal Structure Research Articles

Alloying hBN with aluminum influences absorption and electronic properties

The versatile range of applications for two-dimensional (2D) materials has encouraged scientists to engineer their properties. This is often accomplished by stacking atomically thin layered materials into complex van der Waals heterostructures. A less popular but technologically promising approach is alloying 2D materials. In this work, we demonstrate a first step towards tuning the intrinsic electronic properties of hexagonal boron nitride (hBN). We present a series of aluminum alloyed hexagonal boron nitride (hBAlN) samples grown by metal organic vapor phase epitaxy on 2-inch sapphire substrates with varying aluminum concentration. Importantly, the obtained samples revealed a sp2-bonded crystal structure and modifications in interband optical transitions. Optical absorption experiments disclosed two prominent peaks in the excitonic spectral range with absorption coefficients ~ 106 cm− 1. Their peak energies align closely with the energies of indirect and direct bandgap transitions in hBN. The presence of two absorption peaks can be attributed to mixing of electronic states in the K and M conduction band valleys, resulting in a substantial increase in the absorption coefficient for indirect transitions. The observed effects offer insights into hBN-based two-dimensional alloys, highlighting the potential for developing 2D material-based quantum well structures capable of operating in the challenging deep UV spectral range.

Structural basis for psilocybin biosynthesis

Psilocybin shows significant therapeutic potential for psilocybin-assisted psychotherapy in addressing various psychiatric conditions. The biosynthetic approach promises rapid and efficient production of psilocybin. Understanding the enzymes that contribute to the biosynthesis of psilocybin can enhance its production process. In this study, we elucidate the crystal structures of L-tryptophan-specific decarboxylase PsiD in both its apo and tryptamine-bound states, the 4-hydroxytryptamine kinase PsiK bound to its substrate, and several forms of the methyltransferase PsiM in either apo or substrate-bound forms derived from the psychedelic mushroom. Structure-based evaluations reveal the mechanisms of self-cleavage and self-inhibition in PsiD, along with the sequential catalytic steps from 4-hydroxytryptamine to the final compound, psilocybin. Additionally, we showcase the antidepressant properties of biosynthetic intermediates of psilocybin on female mice experiencing depression-like behaviors induced by sub-chronic variable stress. Our studies establish a structural basis for the future biosynthetic production of psilocybin using these enzymes and emphasize the clinical potential of norbaeocystin.

Phylogenetic and structural insights into the origin of C-type lectin Mincle in vertebrates

Our bodies are continuously exposed to injurious insults by infection and tissue damage, which are primarily sensed by innate immune receptors to maintain homeostasis. Among such receptors is macrophage-inducible C-type lectin (Mincle, gene symbol CLEC4E), a member of the C-type lectin receptor (CLR) family, which functions as an immune sensor for both pathogens and damaged self. To monitor these injurious stimuli, Mincle recognizes disaccharide-based pathogen-derived glycolipids and monosaccharide-based intracellular metabolites, such as β-glucosylceramide. Mincle is well-conserved among mammals; however, there are questions that remain unclear, such as from which lower vertebrate did it arise and whether the original ligand was self or non-self. Here, we found homologues of Mincle and its signaling subunit Fc receptor γ chain (FcRγ) in lower vertebrates, such as reptiles, amphibians, and fishes. The crystal structure of a Mincle homologue revealed that fish Mincle possesses a narrower sugar-binding pocket than that of mammalian Mincle, and accommodates only monosaccharide moieties. These results suggest that Mincle may have evolved from a self-recognizing receptor, and its sugar-binding pocket widened during evolution, presumably to adapt to disaccharide-based glycolipids derived from life-threatening pathogens.

Optimizing Carbon Coating Process for Lithium-Rich LiFePO4 Cathode Materials.

Li1+xFe1-xPO4 (Li-rich LFP) has been proposed as an alternative to address low ionic and electronic conductivity of stoichiometric LiFePO4 (LFP). However, comprehensive studies investigating the impact of the carbon coating process on crystal structure and electrochemical performance during the synthesis of Li-rich LFP are still lacking. In particular, the characteristics of carbon precursor and calcination atmosphere significantly influence formation of crystal structure and electrochemical properties of the Li-rich LFP, underlining the necessity for further investigation. In this study, we compare two synthesis process: introducing carbon precursor before formation of LFP crystal structure (C/BLF) and adding it an additional calcination step after structure has formed (C/ALF). The C/ALF process sample has a larger unit cell volume and denser coating layer. As a result, the C/ALF sample exhibits a lower overpotential (0.54 V) and a higher discharge capacity (~134.13 mAhg-1) than C/BLF sample. These findings elucidate the influence of carbon coating process sequence on crystal structure and electrochemical performance during the synthesis of Li-rich LFP.

First-principles calculations of the mechanical, electronic, and thermal properties of Cr3XN (X = Ga, Pd, Pt, Sn, As, Ge) type materials with anti-perovskite structure

Abstract In this article, the crystal structures, mechanical and other physical properties of anti-perovskite structure Cr3XN (X=Ga, Pd, Pt, Sn, As, Ge) materials were systematically studied by adopting first-principles calculation. The determined lattice parameter exhibits a discrepancy of under 2% when contrasted with the values reported in the existing literature. The formation of energy and phonon spectrum illustrates the stability of materials. At the same time, the elastic modulus and hardness of Cr3XN materials were calculated. The findings reveal that Cr3PtN exhibits a remarkable theoretical hardness of 18.38 G Pa, coupled with a pronounced degree of anisotropy. At the same time, the stress-strain calculation indicated that the Cr3PtN material has the strongest resistance to tensile and compressive strain. According to band structures, anti-perovskite structures of Cr3XN-type materials were all conductors. The electronic density of states comes to the same conclusion. The thermal properties of Cr3XN materials are also calculated. The Debye temperature calculation results indicated that the Cr3GeN material has the best thermal conductivity. However, the Cr3PdN material has the worst thermal conductivity. The calculation results offer theoretical guidance for the practical application of anti-perovskite structure Cr3XN-type materials.

Theoretical Study of (La, Mn) Codoping on the Modification of Photonic Performance in BaTiO3 Materials.

This study aimed to investigate the structure, electronic, ferroelectric, and optical properties of primitive BaTiO3 (BTO) and (Ba0.875La0.125)(Ti0.875Mn0.125)O3 (BLTM) using density functional theory and the generalized gradient approximation plane wave pseudopotential technique. Co-doping with (La, Mn) reduces the tetragonality of BTO, resulting in a pseudocubic configuration of its unit cell. The incorporation of dopant elements introduces impurity levels within the material's band structure, thereby reducing the bandgap and enhancing its light absorption capability. Simultaneously, BLTM exhibits low effective carrier mass and high electrical conductivity. Analysis of its optical properties reveals a high absorption coefficient and pronounced photorefractivity, with a red shift in the absorption peak, demonstrating high absorption rates in both the infrared and visible light regions. The results show that the differences in the ionic radius and electronegativity of the dopant elements lead to changes in the crystal structure and chemical bonding properties of the materials, which in turn affect the electron cloud density of the materials and ultimately effectively improve the material properties.

A low-temperature, one-step synthesis for monazite can transform monazite into a readily usable advanced nuclear waste form.

It has been demonstrated that monazite-type materials are excellent candidates for nuclear waste forms, and hence, their facile synthesis is of great importance for the needed sequestration of existing nuclear waste. The synthesis of monazite, LaPO4, requires inconveniently high temperatures near 1000°C and generally involves the conversion of the presynthesized rhabdophane, LaPO4•nH2O, to the LaPO4 monazite phase. During this structure transformation, the rhabdophane converts irreversibly to the thermodynamically stable monoclinic monazite structure. A low-temperature (185° to 260°C) mild hydrothermal acid-promoted synthesis of monazite is described that can both transform presynthesized rhabdophane or assemble reagents to the monoclinic monazite structure. The pH dependence of this reaction is detailed, and its applicability to the LnPO4 (Ln=La, Ce, Pr, Nd, Sm-Gd), Ca0.5Th0.5PO4, and Sr0.5Th0.5PO4 systems is discussed. The crystal growth of Ca0.5Th0.5PO4 and Sr0.5Th0.5PO4 is described, and their crystal structures were reported. In situ x-ray diffraction studies, performed as a function of temperature, provide insight into the structure transformation process.

The conserved Spd-2/CEP192 domain adopts a unique protein fold to promote centrosome scaffold assembly.

Centrosomes form when centrioles assemble pericentriolar material (PCM) around themselves. Spd-2/CEP192 proteins, defined by a conserved "Spd-2 domain" (SP2D) comprising two closely spaced AspM-Spd-2-Hydin (ASH) domains, play a critical role in centrosome assembly. Here, we show that the SP2D does not target Drosophila Spd-2 to centrosomes but rather promotes PCM scaffold assembly. Crystal structures of the human and honeybee SP2D reveal an unusual "extended cradle" structure mediated by a conserved interaction interface between the two ASH domains. Mutations predicted to perturb this interface, including a human mutation associated with male infertility and Mosaic Variegated Aneuploidy, disrupt PCM scaffold assembly in flies. The SP2D is monomeric in solution, but the Drosophila SP2D can form higher-order oligomers upon phosphorylation by PLK1 (Polo-like kinase 1). Crystal-packing interactions and AlphaFold predictions suggest how SP2Ds might self-assemble, and mutations associated with one such potential dimerization interface markedly perturb SP2D oligomerization in vitro and PCM scaffold assembly in vivo.

Reengineering of Circularly Permuted Caspase-2 to Enhance Enzyme Stability and Enable Crystallographic Studies.

Caspase activation has been linked to several diseases, including cancer, neurodegeneration, and inflammatory conditions, generating interest in targeting this family of proteases for drug development. Caspase-2 (Casp2) in particular has been implicated in Alzheimer's Disease (AD) by cleaving tau protein into fragment Δtau314, which reversibly impairs cognitive and synaptic function. Thus, Casp2 inhibition could be a useful strategy for therapeutic treatment of AD. To that end, we have previously synthesized and characterized various series of peptide and peptidomimetic inhibitors that demonstrate potency and selectivity for Casp2 over caspase-3 (Casp3). Despite promising developments in the design of selective Casp2 inhibitors, low expression yields of Casp2 hinder crystallographic experiments and make structure-based design challenging. The design of circularly permuted (cp) Casp2 increased protein yields considerably; however, this protein could not be crystallized. This article describes the characterization of ten novel cpCasp2 mutants, designed with the goal of increasing stability and facilitating crystallization. Gratifyingly, engineered mutant JF1cpCasp2 displayed high relative stability and was readily crystallizable with the canonical Casp2 inhibitor AcVDVAD-CHO, leading to what we believe to be the first crystal structures of any reverse caspase in the PDB. Moreover, we have reported the structure of JF1cpCasp2 with our recently described Casp2-selective inhibitor MUR-65, which revealed a unique interaction with Arg417 in the binding pocket. Overall, JF1cpCasp2 has proven valuable for structure-based design and expanding understanding of Casp2 inhibition, with potential implications for drug discovery and the development of more selective compounds.

Syntheses, Crystal Structures and Antimicrobial Activity of NiII, ZnII and MnIII Complexes Derived from N,N'-Bis(4-bromosalicylidene)propane-1,2-diamine.

Four new nickel(II), zinc(II) and manganese(III) complexes, [NiL] (1), [Zn3L2(OAc)2] (2), [ZnL(CH3OH)] (3) and [MnClL(DMF)] (4), derived from the bis-Schiff base N,N'-bis(4-bromosalicylidene)propane-1,2-diamine (H2L) have been prepared and characterized by spectroscopy methods, as well as single crystal X-ray determination. The Ni atom in the mononuclear nickel complex 1 is in square planar coordination. The outer and inner Zn atoms in the trinuclear zinc complex 2 are in square planar and octahedral coordination, respectively. The Zn atom in the mononuclear zinc complex 3 is in square pyramidal coordination. The Mn atom in the mononuclear manganese complex 4 is in octahedral coordination. Antibacterial activity of the complexes has been assayed on the bacteria Staphylococcus aureus and Escherichia coli, and the yeast Candida parapsilosis.

Synthesis, Crystal Structures and Catalytic Oxidation Property of Two Copper(II) Complexes Derived from 5-Bromo-2-((2-piperazin-1-ylethylimino)methyl)phenol.

Two new copper(II) complexes, [Cu(HL)(ONO2)]NO3 (1) and [CuCl(HL)]Cl∙H2O (2), where HL is the zwitterionic form of the Schiff base 5-bromo-2-((2-piperazin-1-ylethylimino)methyl)phenol (HL), have been prepared. The Schiff base and two complexes were characterized by IR and UV-Vis spectroscopy. In addition, the free Schiff base was characterized by 1H NMR spectroscopy. Structures of the complexes were further confirmed by single crystal X-ray diffraction. The Cu atoms in the complexes are in square planar coordination. Crystal structures of both copper complexes are stabilized by hydrogen bonds. The complexes have high catalytic activity for the epoxidation of styrene, with conversions and selectivity over 90%.

Crystal structure, magnetic properties, and tunable Kondo effect in a new compound Nd5ScSb12

Crystal structure, magnetic properties, and tunable Kondo effect in a new compound Nd₅ScSb₁₂

Unveiling the Over-Lithiation Behavior of NCM523 Cathode Towards Long-Life Anode-Free Li Metal Batteries.

Anode-free lithium metal batteries (AFLMBs) offer the potential for significantly enhanced energy densities. However, their practical application is limited by a shortened cycling life due to inevitable Li loss from parasitic reactions. This study addresses this challenge by incorporating an over-lithiated Li1+ xNi0.5Co0.2Mn0.3O2 (Li1+ xNCM523) cathode as an internal Li reservoir to compensate for lithium loss during extended cycling. A rigorous investigation of the deep discharge behavior of the Li1+ xNCM523 cathode reveals a critical over-lithiation threshold at x=0.7. At this threshold, excess Li+ ions are safely accommodated within the crystal structure by a transformation from the LiO4 octahedron to two tetrahedral sites. Beyond this threshold (x ≥ 0.7), the structural stability of the cathode is significantly compromised due to the irreversible reduction of transition metal (TM) ions. The optimal Li-rich Li1.7NCM523 releases an additional charge capacity of ≈160 mAh g-1 during the first charge. Consequently, the AFLMBs (Li1.7NCM523||Cu) achieve outstanding capacity retention of 93.3% after 100 cycles at 0.5 C and 78.5% after 200 cycles at 1 C. The findings establish a research paradigm for designing superior over-lithiated transition metal oxide cathode materials and underscore the critical role of the lithium reservoir in extending the cycle life of AFLMBs.

Synthesis, crystal and electronic structure of Ca4CdIn2Ge4: A quaternary variant of the monoclinic Mg5Si6 structure

Synthesis, crystal and electronic structure of Ca4CdIn2Ge4: A quaternary variant of the monoclinic Mg5Si6 structure

Synthesis, crystal and electronic structure, and thermal behavior of a new flame retardant-hardener [Cu(diethylenetriamine)2]Cl2•H2O for epoxy resins.

A copper(II) chelate complex with diethylenetriamine (deta), [Cu(deta)2]Cl2·H2O (1), was synthesized by direct interaction of solid copper(II) chloride dihydrate with deta. Complex 1 was characterized by X-ray structural analysis, infrared (IR) spectroscopy and differential scanning calorimetry (DSC) and was studied as a flame retardant-hardener for epoxy resins. The crystals of 1 consist of [Cu(deta)2]2+ cations, Cl- anions and uncoordinated water molecules. Each Cu(II) atom is chelated with two tridentate molecules of deta, which bond to the central Cu(II) atom in a non-equivalent manner. This results in a distorted tetragonal bipyramidal environment around the Cu(II) atom. The crystal packing of the structural units in 1 is determined by both the dominant cation-anion interaction and strong hydrogen bonds, such as N-H···Cl, N-H···O, and O-H···Cl. Density functional theory (DFT) calculations were performed to determine the electron structure of 1 using the restricted formalism of B3LYP method with a 6-31G* orbital basis set. The d-orbitals of the Cu2+ ion are split due to the interaction of a tetragonal bipyramidal environment and the chelation, resulting in the visually observed dark blue color of crystals of 1. This color closely corresponds to the calculated value of the visible light wavelength (λ = 661.37 nm), which is related to the energy of photons absorbed by the complex (Δ = 1.874 eV).

Microwave-Assisted Synthesis of Phenyl Quinazoline: Investigation 'ON-OFF-ON' and Latent Fingerprint Applications.

Stimuli-responsive materials with donor-acceptor (D-A) systems have significant potential for sensing toxic analytes in solution and solid state. In this regard, a new probe, N, N-dimethyl-4-(4-phenylquinazolin-2-yl) aniline (DAQ), was synthesized using microwave irradiation and characterized using various spectroscopic techniques. The crystal structure analysis revealed that DAQ crystallized in a monoclinic system with a P21/m space group. The probe exhibits fluorescence properties in solid state and solution, with positive solvatochromism observed as solvent polarity increased from hexane to DMF, indicating the existence of D-A structural units. The probe DAQ, exhibited reversible switching behaviour in the solution and solid state, indicating its sensitivity to volatile trifluoroacetic acid (TFA) and triethylamine (TEA) as confirmed by spectrophotometric and spectrofluorimetric studies. The binding constant of probe DAQ with TFA and TEA were studied by the Benesi Hildebrand (BH) plot using UV-Vis spectral titration. The estimated association constant was found to be 1.43 × 104 M- 1. The DAQ aggregation-enhanced emission properties have been successfully utilized to develop security ink and latent fingerprint information encryption on various substrates in their aggregated solid state. The study reveals that the sensitivity of DAQ warrants application on all forms of forensic evidence.

Metallization without Charge Transfer in CuReO4 Perrhenate under Pressure.

Using high-pressure synchrotron X-ray diffraction combined with Raman spectroscopy and density-functional calculations, we determined the sequence of the pressure-induced transformations in CuReO4. At 1.5 GPa, the lattice symmetry changes from I41cd to I41/a with the transformation of isolated ReO4-tetrahedra into infinite chains of ReO6-octahedra. The second, isosymmetric transition at 7 GPa leads to the formation of a NbO2-type structure with the octahedral oxygen coordination for both Cu1+ and Re7+ cations. Both transitions are of the first order and accompanied by discontinuities in the unit-cell volume of 7 and 14%, respectively. Density-functional calculations predict the metallic state of the high-pressure NbO2-type phase of CuReO4, and this prediction is in-line with the disappearance of the Raman signal above 7 GPa and visual observations (darkness/reflection of the sample). This metallization is caused by the increased bandwidth of both Cu 3d and Re 5d bands without any significant charge transfer between Cu and Re. At ambient pressure, the crystal structure of CuReO4 is retained between 4 and 700 K (melting point), showing a negative thermal expansion along the c-axis and a positive expansion along the a-axis within the entire temperature range.

Narrowed pore conformations of aquaglyceroporins AQP3 and GlpF

Aquaglyceroporins such as aquaporin−3 (AQP3) and its bacterial homologue GlpF facilitate water and glycerol permeation across lipid bilayers. X-ray crystal structures of GlpF showed open pore conformations, and AQP3 has also been predicted to adopt this conformation. Here we present cryo-electron microscopy structures of rat AQP3 and GlpF in different narrowed pore conformations. In n-dodecyl-β-D-maltopyranoside detergent micelles, aromatic/arginine constriction filter residues of AQP3 containing Tyr212 form a 2.8-Å diameter pore, whereas in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) nanodiscs, Tyr212 inserts into the pore. Molecular dynamics simulation shows the Tyr212-in conformation is stable and largely suppresses water permeability. AQP3 reconstituted in POPC liposomes exhibits water and glycerol permeability, suggesting that the Tyr212-in conformation may be altered during permeation. AQP3 Y212F and Y212T mutant structures suggest that the aromatic residue drives the pore-inserted conformation. The aromatic residue is conserved in AQP7 and GlpF, but neither structure exhibits the AQP3-like conformation in POPC nanodiscs. Unexpectedly, the GlpF pore is covered by an intracellular loop, but the loop is flexible and not primarily related to the GlpF permeability. Our findings illuminate the unique AQP3 conformation and structural diversity of aquaglyceroporins.

Multitrack Boosted Hard Carbon Anodes: Innovative Paths and Advanced Performances in Sodium-Ion Batteries.

Sodium-ion batteries (SIBs) are emerging as a potential alternative to traditional lithium-ion batteries due to the abundant sodium resources. Carbon anodes, with their stable structure, wide availability, low cost, excellent conductivity, and tunable morphology and pore structure, exhibit outstanding performance in SIBs. This review summarizes the research progress of hard carbon anodes in SIBs, emphasizing the innovative paths and advanced performances achieved through multitrack optimization, including dimensional engineering, heteroatom doping, and microstructural tailoring. Each dimension of carbon material-0D, 1D, 2D, and 3D-offers unique advantages: 0D materials ensure uniform dispersion, 1D materials have short Na+ diffusion paths, 2D materials possess large specific surface areas, and 3D materials provide e-/Na+ conductive networks. Heteroatom doping with elements such as N, S, and P can tune electronic distribution, expand interlayer spacing of carbon, and induce Fermi level shifts, thereby enhancing sodium storage capability. In addition, defect engineering improves electrochemical performance by modifying graphitic crystal structure. Furthermore, suitable pore structure design, particularly closed pore structures, can increase capacity, minimizes side reactions, and suppress degradation. In future studies, optimizing morphology design, exploring heteroatom co-doping, and developing environmentally friendly, low-cost carbon anode methods will drive the application of high-performance and long cycle life SIBs.

Theoretcial Investigation on Reaction Mechanism of Binuclear Nickel Guanidine Hydrolase

The nitrogen‐rich compound guanidine is widely distributed in nature, but its utilization is hindered by strong resonance stabilization. GdmH, a binuclear nickel enzyme from Synechocystis sp. PCC 6803, is capable of directly converting guanidinium cation into urea and ammonium. In this study, we employed density functional calculations to investigate the reaction mechanism of GdmH using a chemical model derived from the enzyme's X‐ray crystal structure. The calculations revealed that the GdmH‐catalyzed guanidinium hydrolysis proceeds through a nucleophilic attack by the di‐nickel bridging hydroxide on the guanidinium carbon forming a tetrahedral intermediate, two proton transfer steps from the hydroxyl to an amino facilitated by Asp203, C‐N bond cleavage yielding urea and ammonia, and regeneration of the bridging hydroxide accompanied by ammonium release. The rate‐limiting step is the first proton transfer from hydroxyl to Asp203, with an energy barrier of 11.8 kcal/mol. Comparative analyses demonstrated that neutral guanidine cannot be hydrolyzed by GdmH due to the absence of a positive charge, which is essential for effective catalysis. Further investigations showed that GdmH is inefficient in catalyzing urea hydrolysis. These findings enhance our understanding of the catalytic specificity of GdmH and the role of nickel cofactors in biological enzymatic processes.