Crystal Structure Research Articles

Anharmonic and quantum effects in Pm3̄ AlM(M = Hf, Zr)H6 under high pressure: A first-principles study.

First-principles calculations were employed to investigate the impact of quantum ionic fluctuations and lattice anharmonicity on the crystal structure and superconductivity of Pm3̄ AlM(M = Hf, Zr)H6 at pressures of 0.3-21.2GPa (AlHfH6) and 4.7-39.5GPa (AlZrH6) within the stochastic self-consistent harmonic approximation. A correction is predicted for the crystal lattice parameters, phonon spectra, and superconducting critical temperatures, previously estimated without considering ionic fluctuations on the crystal structure and assuming the harmonic approximation for lattice dynamics. The findings suggest that quantum ionic fluctuations have a significant impact on the crystal lattice parameters, phonon spectra, and superconducting critical temperatures. Based on our anharmonic phonon spectra, the structures will be dynamically stable at 0.3GPa for AlHfH6 and 6.2GPa for AlZrH6, ∼6 and 7GPa lower than pressures given by the harmonic approximation, respectively. Due to the anharmonic correction of their frequencies, the electron-phonon coupling constants (λ) are suppressed by 28% at 11GPa for AlHfH6 and 22% at 30GPa for AlZrH6, respectively. The decrease in λ causes Tc to be overestimated by ∼12K at 11GPa for AlHfH6 and 30GPa for AlZrH6. Even if the anharmonic and quantum effects are not as strong as those of Pm3̄n-AlH3, our results also indicate that metal hydrides with hydrogen atoms in interstitial sites are subject to anharmonic effects. Our results will inevitably stimulate future high-pressure experiments on synthesis, structural, and conductivity measurements.

The crystal structure of Shethna protein II (FeSII) from Azotobacter vinelandii suggests a domain swap.

The Azotobacter vinelandii FeSII protein forms an oxygen-resistant complex with the nitrogenase MoFe and Fe proteins. FeSII is an adrenodoxin-type ferredoxin that forms a dimer in solution. Previously, the crystal structure was solved [Schlesier et al. (2016), J. Am. Chem. Soc. 138, 239-247] with five copies in the asymmetric unit. One copy is a normal adrenodoxin domain that forms a dimer with its crystallographic symmetry mate. The other four copies are in an `open' conformation with a loop flipped out exposing the 2Fe-2S cluster. The open and closed conformations were interpreted as oxidized and reduced, respectively, and the large conformational change in the open configuration allowed binding to nitrogenase. Here, the structure of FeSII was independently solved in the same crystal form. The positioning of the atoms in the unit cell is similar to the earlier report. However, the interpretation of the structure is different. The `open' conformation is interpreted as the product of a crystallization-induced domain swap. The 2Fe-2S cluster is not exposed to solvent, but in the crystal its interacting helix is replaced by the same helix residues from a crystal symmetry mate. The domain swap is complicated, as it is unusual in being in the middle of the protein rather than at a terminus, and it creates arrangements of molecules that can be interpreted in multiple ways. It is also cautioned that crystal structures should be interpreted in terms of the contents of the entire crystal rather than of one asymmetric unit.

Crystal structure and cryomagnetic study of a mononuclear erbium(III) oxamate inclusion complex.

The synthesis, crystal structure and magnetic properties of an oxamate-containing erbium(III) complex, namely, tetrabutylammonium aqua[N-(2,4,6-trimethylphenyl)oxamato]erbium(III)-dimethyl sulfoxide-water (1/3/1.5), (C16H36N)[Er(C11H12NO3)4(H2O)]·3C2H6OS·1.5H2O or n-Bu4N[Er(Htmpa)4(H2O)]·3DMSO·1.5H2O (1), are reported. The crystal structure of 1 reveals the occurrence of an erbium(III) ion, which is surrounded by four N-phenyl-substituted oxamate ligands and one water molecule in a nine-coordinated environment, together with one tetrabutylammonium cation acting as a counter-ion, and one water and three dimethyl sulfoxide (DMSO) molecules of crystallization. Variable-temperature static (dc) and dynamic (ac) magnetic measurements were carried out for this mononuclear complex, revealing that it behaves as a field-induced single-ion magnet (SIM) below 5.0 K.

Na[GeF5]·2HF: the first quarternary phase in the H-Na-Ge-F system.

The structure of cis- or trans-bridged [GeF5]- anionic chains have been investigated [Mallouk et al. (1984). Inorg. Chem. 23, 3160-3166] showing the first crystal structures of μ-F-bridged pentafluorogermanates. Herein, we report the second crystal structure of trans-pentafluorogermanate anions present in the crystal structure of sodium trans-pentafluorogermanate(IV) bis(hydrogen fluoride), Na[GeF5]·2HF. The crystal structure [orthorhombic Pca21, a= 12.3786 (3), b= 7.2189 (2), c= 11.4969 (3) Å and Z= 8] is built up from infinite chains of trans-linked [GeF6]2- octahedra, extending along the b axis and spanning a network of pentagonal bipyramidal distorted Na-centred polyhedra. These [NaF7] polyhedra are linked in a trans-edge fashion via hydrogen fluoride molecules, in analogy to already known sodium hydrogen fluorides and potassium hydrogen fluorides.

Crystal structure, supramolecular framework, hirshfeld surface analysis, and photophysical studies of some acridinium/acridine derivatives prepared by mechanochemical synthesis

Crystal structure, supramolecular framework, hirshfeld surface analysis, and photophysical studies of some acridinium/acridine derivatives prepared by mechanochemical synthesis

A highly stable insertion type V1-xTixP solid solution as an anode material for high-rate lithium-ion batteries

As electric vehicles (EVs) grow in popularity, the demand for lithium-ion batteries (LIBs) simultaneously grows, and the fast-charging capability is becoming increasingly important. However, it is generally believed that graphite anode still suffers from a poor rate capability for fast-charging applications, and other insertion-type oxide anodes with a high rate capability exhibit too high Li+-ion insertion/extraction potential, which cannot meet a requirement for high energy density anodes. In this work, the hexagonal structure of V1-xTixP (x = 0.0, 0.25, and 1.0) phases were introduced as insertion-type anode materials for LIBs with a low reaction potential of Li+-ion insertion/extraction. The crystal structure and the corresponding electrochemical reaction mechanism of insertion-type anodes of TiP, VP, and MoP were compared. A facile strategy forming a substitutional solid solution is suggested to improve the electrochemical properties of anode materials by combining the end members among insertion-type VP, TiP, and MoP as forming V1-xTixP and V1-xMoxP compounds. V1-xTixP (x = 0.25) electrode, substituting V atoms with Ti atoms in VP structure, shows excellent long-term cycle stability at 1 A/g with a cycle retention of 87.7 % during 2500 cycles, delivering a two times higher capacity of 211.1 mAh g−1 compared to that of the commercial graphite electrode.

A new inhibitor of quaternary copolymer against calcium carbonate scaling in high-temperature geothermal fluids

An effective quaternary copolymer inhibitor against calcium carbonate scaling in 120 °C geothermal fluids, with an inhibition ratio of over 95 %, was synthesized through aqueous free radical polymerization of itaconic acid (IA), acrylic acid (AA), hydroxy ethyl methacrylate (HEMA), and sodium allylsulfonate (SAS). The synthesis process involved using ammonium persulfate as an initiator and tert-butanol as the molecular weight regulator. A four-factor, three-level orthogonal experiment was conducted to optimize the synthesis process, resulting in a monomer ratio of m(IA):m(AA) = 1:7, 15 % initiator concentration, a reaction temperature of 90 °C, and a reaction time of 2.5 h. Fourier transform infrared spectroscopy (FT-IR) analysis revealed the presence of carboxyl, sulfonic acid, hydroxyl, and ester groups in the copolymer, while thermogravimetric analysis (TGA) confirmed its thermal stability. Scanning electron microscopy (SEM) and X-ray diffraction (XRD) examinations of calcium carbonate crystals indicated that the copolymer scale inhibitor caused significant damage to the surface morphology and crystal structure. This scaling inhibitor is useful for efficient geothermal energy utilization.

Enhancing photoluminescence of WSe2 in vapor grown WSe2/VOCl bilayer heterojunctions via surface passivation.

Monolayer tungsten selenide (WSe2) has attracted attention due to its direct bandgap-generated strong light emission and light-matter interaction. Herein, vertical WSe2/VOCl bilayer heterojunctions with enhanced PL of WSe2 were synthesized by the vapor growth method. The morphology, crystal structure, and chemical composition of the WSe2/VOCl heterojunctions were systematically investigated, which confirmed the successful formation of the heterojunctions. The PL emission intensity of WSe2 obtained from the WSe2/VOCl heterojunction was about 2.4 times higher than that of the WSe2 monolayer, demonstrating the high optical quality of the WSe2/VOCl heterojunction, which was further confirmed by time-resolved PL measurements. The insulator top VOCl, which was deposited on the surface of the semiconductor bottom WSe2 as a surface passivation material, reducing the impurities and resulting in an atomically clean surface, successfully enhanced the PL emission of the bottom WSe2. This vertical WSe2/VOCl bilayer heterojunction with PL enhancement could provide a promising platform for optical devices.

Combined X-ray Diffraction Analysis and Quantum Chemical Interpretation of the Effect of Thermal Neutrons on the Geometry and Electronic Properties of CdTe

Objective: Substantiation of the result of the interaction of thermal neutrons with CdTe crystals by quantum-chemical methods and comparison of the experimental results with the results of quantum-chemical calculations. Methods: Single crystal samples of cadmium telluride (CdTe) were obtained by a modified Bridgman method. The plates cut from the single crystal were subjected to mechanical grinding with abrasive paper of the type P1,200-P4,000, mechanical polishing with silver paste. To clean the surface of the plate from contamination, it was washed in ethyl alcohol. In the experimental part of the work, the influence of low thermal neutron fluxes on the structural parameters of CdTe was studied. The samples were irradiated with a thermal neutron flux in the range from 2.64×107 neutron/cm2 to 1.85×109 neutron/cm2. To study the structure of CdTe crystals, the method of X-ray structural analysis was used, using a DRON-3 X-ray diffractometer. In the second part of the work, computer modeling of the process of interaction of thermal neutrons on CdTe crystals was carried out. Results: X-ray diffraction analysis of the crystals showed that as a result of irradiation with low thermal neutron fluxes, the structural parameters of CdTe improve, as evidenced by the ordering of the crystallites. In addition, in this region of the thermal neutron flux the resistance of the crystals decreases. Conclusion: Calculations of the crystal lattice parameters of CdTe are in good agreement with experimental data. The electronic and optical properties of CdTe have been studied. A decrease in the band gap after irradiation with thermal neutrons has been shown.

Crystallographic Pathways to Tailoring Metal-Insulator Transition through Oxygen Transport in VO2.

The metal-insulator (MI) transition of vanadium dioxide (VO2) is effectively modulated by oxygen vacancies, which decrease the transition temperature and insulating resistance. Oxygen vacancies in thin films can be driven by oxygen transport using electrochemical potential. This study delves into the role of crystallographic channels in VO2 in facilitating oxygen transport and the subsequent tuning of electrical properties. A model system is designed with two types of VO2 thin films: (100)- and (001)-oriented, where channels align parallel and perpendicular to the surface, respectively. Growing an oxygen-deficient TiO2 layer on these VO2 films prompted oxygen transport from VO2 to TiO2. Notably, in (001)-VO2 film, where oxygen ions move along the open channels, the oxygen migration deepens the depleted region beyond that in (100)-VO2, leading to more pronounced changes in metal-insulator transition behaviors. The findings emphasize the importance of understanding the intrinsic crystal structure, such as channel pathways, in controlling ionic defects and customizing electrical properties for applications.

Crystallographic Pathways to Tailoring Metal-Insulator Transition through Oxygen Transport in VO2.

The metal-insulator (MI) transition of vanadium dioxide (VO2) is effectively modulated by oxygen vacancies, which decrease the transition temperature and insulating resistance. Oxygen vacancies in thin films can be driven by oxygen transport using electrochemical potential. This study delves into the role of crystallographic channels in VO2 in facilitating oxygen transport and the subsequent tuning of electrical properties. A model system is designed with two types of VO2 thin films: (100)- and (001)-oriented, where channels align parallel and perpendicular to the surface, respectively. Growing an oxygen-deficient TiO2 layer on these VO2 films prompted oxygen transport from VO2 to TiO2. Notably, in (001)-VO2 film, where oxygen ions move along the open channels, the oxygen migration deepens the depleted region beyond that in (100)-VO2, leading to more pronounced changes in metal-insulator transition behaviors. The findings emphasize the importance of understanding the intrinsic crystal structure, such as channel pathways, in controlling ionic defects and customizing electrical properties for applications.

Detection of ethanol gas at room temperature by In2O3-based screen-printed films fabricated through particle-free aqueous solution combustible inks

Abstract The current work investigates the room temperature ethanol gas detection capabilities of pristine, Sn doped, Zn doped, Sn & Zn co-doped In2O3-based screen-printed films that are developed using particle-free aqueous solution combustible inks. The fabricated films were pure, polycrystalline with cubic bixbyite crystal structure, porous, and transparent (~75 to 95 % in the visible range). High surface roughness was detected in pristine film than in doped films. Ethanol gas of 50 to 100 ppm concentration was traced by all the films at room temperature. Among all, the pristine film showed a greater gas response at all concentrations of ethanol gas, and it was because of high oxygen vacancy concentration (OV/OL) and more relative area fraction of adsorbed oxygen (% of OA). Diminished amounts of OV/OL and % of OA caused a relatively low gas response in the doped films. The maximum ethanol gas response was discerned to be 17.3 at 100 ppm by the pristine film. The demonstrated film was also highly selective towards ethanol gas.

Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen.

T cell receptor (TCR) recognition of foreign peptides presented by major histocompatibility complex protein is a major event in triggering the adaptive immune response to pathogens or cancer. The prediction of TCR-peptide interactions has great importance for therapy of cancer as well as infectious and autoimmune diseases but remains a major challenge, particularly for novel (unseen) peptide epitopes. Here we present TCRen, a structure-based method for ranking candidate unseen epitopes for a given TCR. The first stage of the TCRen pipeline is modeling of the TCR-peptide-major histocompatibility complex structure. Then a TCR-peptide residue contact map is extracted from this structure and used to rank all candidate epitopes on the basis of an interaction score with the target TCR. Scoring is performed using an energy potential derived from the statistics of TCR-peptide contact preferences in existing crystal structures. We show that TCRen has high performance in discriminating cognate versus unrelated peptides and can facilitate the identification of cancer neoepitopes recognized by tumor-infiltrating lymphocytes.

Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen.

T cell receptor (TCR) recognition of foreign peptides presented by major histocompatibility complex protein is a major event in triggering the adaptive immune response to pathogens or cancer. The prediction of TCR-peptide interactions has great importance for therapy of cancer as well as infectious and autoimmune diseases but remains a major challenge, particularly for novel (unseen) peptide epitopes. Here we present TCRen, a structure-based method for ranking candidate unseen epitopes for a given TCR. The first stage of the TCRen pipeline is modeling of the TCR-peptide-major histocompatibility complex structure. Then a TCR-peptide residue contact map is extracted from this structure and used to rank all candidate epitopes on the basis of an interaction score with the target TCR. Scoring is performed using an energy potential derived from the statistics of TCR-peptide contact preferences in existing crystal structures. We show that TCRen has high performance in discriminating cognate versus unrelated peptides and can facilitate the identification of cancer neoepitopes recognized by tumor-infiltrating lymphocytes.

Novel base‐catalyzed acylation of benzenediols with vinyl acetate: a Hirshfeld surface study

AbstractBACKGROUNDThe present work describes the facile, fast and economic base‐catalyzed acylation of benzenediols with vinyl acetate. The Hirshfeld surface analysis of benzene‐1,4‐diol O,O′‐diacetate is also described. NaOH, KOH and K2CO3 were the bases used for the catalysis of the acylation of benzene‐1,x‐diols (x = 2, 3, 4) with vinyl acetate to obtain the corresponding O,O′‐diacetyl derivatives.RESULTSThe yields were quite good, up to 99% under solvent‐free conditions. This method represents an alternative ‘green’ process for the preparation of O‐acetyl derivatives of hydroxyaryls. The benzene‐1,4‐diol O,O′‐diacetate crystal structure was obtained and described using Hirshfeld surface analysis. A noticeable contribution of the C⋯H contacts is shown (16.7%), despite the insignificant area of the Hirshfeld surface occupied by the carbon atoms (9.4%). By using two‐dimensional fingerprint plots, it was proved that C⋯H contacts were due to the presence of π‐stacking. The O⋯H contacts (41.4%) were the most numerous ones, relating mainly to typical hydrogen bonds (de + di ≈ 2.6 Å). The high saturation of the C⋯H and O⋯H contacts (enrichment ratios (E) = 1.30 and 1.36, respectively), despite their smaller contribution to the overall surface as compared to the H⋯H contacts (E = 0.84), is shown.CONCLUSIONThe novelty of this work is the development of a method based on an inexpensive, safe and easy‐to‐use catalyst (K2CO3). This method is fast with high yields. Besides, it may be used for acylation at an industrial scale. © 2024 Society of Chemical Industry (SCI).

A novel one-dimensional thiocyanate-bridged cobalt(III) complex: synthesis, crystal structure characterization and Hirshfeld surface analysis.

A new one-dimensional thiocyanate-bridged cobalt(III) Schiff base complex, namely, catena-poly[[[4-bromo-2-((Z)-{[2-(thiophen-2-yl)ethyl]imino}methyl)phenolato-κ2N,O]cobalt(III)]-μ-thiocyanato-κ2N:S], [Co(SCN)(C13H11BrNOS)2]n or [Co(μ1,3-SCN)L2]n (1), where HL is 4-bromo-2-((Z)-{[2-(thiophene-2-yl)ethyl]imino}methyl)phenol, a bidentate Schiff base prepared from the condensation reaction of 5-bromosalicylaldehyde and 2-(thiophen-2-yl)ethylamine, has been synthesized by stirring Co(ClO4)2·6H2O, the Schiff base HL and ammonium thiocyanate (in a 1:2:1 molar ratio) in ethanol medium. The complex was characterized by FT-IR, electronic spectra and single-crystal X-ray diffraction (SC-XRD) studies. The SC-XRD data suggest that the compound crystallizes in the orthorhombic space group Pca21. The CoIII ion in 1 adopts a distorted octahedral geometry, the metal sites being six-coordinated by one thiocyanate N atom and one thiocyanate S atom in apical positions, and by two imine N atoms and two phenolate O atoms from two anionic L- ligands which form the basal plane. The thiocyanate ligand acts as a μ-1,3 bridge, joining neighbouring CoIII atoms and forming a uniform zigzag one-dimensional polymeric chain. The crystallographic data were also used in the Hirshfeld surface (HS) analysis, which aimed to investigate the nature and quantitative significance of any noncovalent intermolecular interactions inside the crystal lattice. The crystal void parameters have also been computed and show the molecules to be tightly packed.

Screening, Synthesis, and Characterization of a More Rapidly Dissolving Celecoxib Crystal Form.

The prevalence of poor solubility in active pharmaceutical ingredients (APIs) such as celecoxib (CEL) is a major bottleneck in the pharmaceutical industry, leading to a low concentration gradient, poor passive diffusion, and in vivo failure. This study presents the synthesis and characterization of a new cocrystal of the API CEL. CEL is a nonsteroidal anti-inflammatory drug used for the treatment of osteoarthritis and rheumatoid arthritis. Computational screening was completed for CEL against a large library of generally recognized as safe (GRAS) coformers, based on molecular complementarity and hydrogen bond propensity (HBP). The generated list of 17 coformers with a likelihood for cocrystallization with CEL were experimentally screened using four techniques: liquid-assisted grinding (LAG), solvent evaporation (SE), gas antisolvent crystallization (GAS), and supercritical enhanced atomization (SEA). One new crystalline form was isolated, employing the liquid coformer N-ethylacetamide (NEA). This novel form, celecoxib-di-N-ethylacetamide (CEL·2NEA), was characterized by a variety of different techniques. The crystal structure was determined through single-crystal X-ray diffraction. Both NEA molecules are evolved from the crystal structure at a desolvation temperature of approximately 65 °C. The CEL·2NEA cocrystal exhibited a dissolution rate, with more than a twofold improvement in comparison to as-received CEL after only 15 min.

A Novel Family of Luminescent Pyrenyl‐(N‐Heterocyclic Carbene)‐ Halogenated Coinage Metal Complexes: Synthesis, Crystal Structures, and Optical Properties

A family of luminescent pyrenyl‐(NHC)‐M‐Cl coinage metal complexes has been prepared and fully characterized (NHC = N‐heterocyclic carbene). Two classes of complexes are described: (M = Cu (1a), Ag (2a), Au (3a) where pyrenyl‐(NHC) = 1‐pyrenyl‐3‐methyl‐Imidazolin‐2‐ylidene and M = Cu (1b), Ag (2b), Au (3b) with pyrenyl‐(NHC) = 1‐pyrenyl‐3‐naphthyl‐Imidazolin‐2‐ylidene. The molecular structures of the six complexes were confirmed by single crystal X‐ray diffraction studies. All complexes were found to be emissive in solution and solid state. The use of the chromophoric‐(NHC) ligand endows to these complexes emissive properties in solution in the blue region (376‐397nm). The presence of the naphthyl‐substituent in the 1b‐3b series enhances the quantum yields relative to the methyl‐series 1a‐3a. In particular, the carbene gold complexes were the most emissive and displayed the highest quantum yields

Pharmacophore-based virtual screening of commercial databases against β-secretase 1 for drug development against Alzheimer’s disease

β-secretase 1, one of the most important proteins, is an aspartate protease. This membrane-associated protein is used for treating Alzheimer’s disease (AD). Several inhibitors have been pursued against β-secretase 1, but they still have not resulted effectively. Virtual screening based on pharmacophores has been shown to be useful for lead optimization and hit identification in the preliminary phase of developing a new drug. Here, we screen the commercially available databases to find the hits against β-secretase 1 for drug discovery against AD. Virtual screening for 200,000 compounds was done using the database from the Vitas-M Laboratory. The phase screen score was utilized to assess the screened hits. Molecular docking was performed on compounds with phase scores >1.9. According to the study, the 66H ligand of the crystal structure has the maximum performance against β-secretase 1. The redocking of the co-crystal ligand showed that the docked ligand was seamlessly united with the crystal structure. The reference complex had three hydrogen bonds with Asp93, Asp289, and Gly291; one van der Waals interaction with Gly74; and three hydrophobic interactions. After equilibration, the RMSD of the reference compound sustained a value of ∼1.5 Å until 30 ns and then boosted to 2.5 Å. On comparison, the RMSD of the S1 complex steadily increased to ∼2.5 Å at 15 ns, displayed slight aberrations at approximately ∼2.5–3 Å until 80 ns, and then achieved steadiness toward the end of the simulation. The arrangements of proteins stayed condensed during the mockup when bonded to these complexes as stable Rg values showed. Furthermore, the MM/GBSA technique was employed to analyze both compounds’ total binding free energies (ΔGtotal). Our research study provides a new understanding of using 66H as anti-β-secretase 1 for drug development against AD.

Stabilization of Short- and Long-Range Magnetic Orderingthrough the Cooperative Effect of 1D [CuO4] Chainsand [CuO2X2] Quadrilateral in Quasi-1D Spin-1/2 Systems.

Quasi-1D chain antiferromagnetswith reduced structural dimensionality area rich playground for investigating novel quantum phenomena. We report the synthesis, crystal structure, and magnetism of two novel quasi-1D antiferromagnets, β-PbCu2(TeO3)2Cl2 (I) and PbCu2(TeO3)2Br2 (II).Their magnetic frameworks are constructed via Cu-based quasi-1D [Cu(2)O4]zigzagchains with square-planar [Cu(1)O2X2] (X = Cl or Br) separated among 1D chains. Specific heat measurements show l peaks at ~9 K and ~19 Kfor I and II, respectively. Moreover, both broad maximums (χmax = 90 K for I and 80 K for II) and small kinks (TN ≈ 9 K for I and 19 K for II) have been observed in magnetic susceptibility measurements of I and II. Bonner-Fisher model fitting, and theoretical analyses were performed to evaluate the magnetic exchange interactions. Our experimental and theoretical results and structure-properties relationship analysis reveal the coexistence of short-and long-range magnetic ordering from the cooperative effect of 1D [CuO4]chains and [CuO2X2] quadrilateral.