Crystal Structure Research Articles

Kinetics-Driven Crystal Facet Evolution Mechanism of Atomically Ordered Intermetallic PtFe Nanocubes toward Electrochemical Catalysis.

Crystal structure engineering in nanoparticles has been regarded as a vital method in catalyst development and design. Herein, PtFe nanocubes, manufactured with ordered PtFe intermetallic structure and a desired facet of {202}, have been successfully prepared via the combination of selective deposition strategy and spatial barrier effect. In-situ X-ray photoelectron spectroscopy found that the growth of the high-index facet and formation of the nanocube for o-PtFe-202 materials arise from the surface Fe2+ modification stabilized effect and the selective deposition of Cl-, respectively. Moreover, density functional theory calculations and X-ray adsorption spectroscopies further proved that the improved oxygen reduction reaction activity and stability of o-PtFe-202 mainly originate from the synergistic effect of the desired high-index facet, ordered crystal structure, and resulting optimal d-band center of Pt. As expected, the o-PtFe-202 exhibits excellent mass activity (2.48 mA·ugPt-1) and specific activity (7.78 mA·cm-2), with only a 7.3% decrease in mass activity after 30 000 cycles.

Improvement of Single-Crystal Structures of Very Heavy Element Compounds by Refining Anomalous Dispersion Parameters.

Refining the anomalous dispersion parameters of the four uranium compounds NaUF5, NaU2F9, Cs2(UO2)TiO4, and Cs2(UO2)Ti2O6 gave insights into the crystallographic model improvement of very heavy atoms. We found that the values for the dispersive and absorptive parts, f' and f″, closely followed the X-ray absorption spectra on their L3, L2, and L1 edges. The obtained values are sensitive to the chemical environment at each crystallographically independent position. An incorrect treatment of the anomalous dispersion correction can lead to a wrong crystallographic model. The above-mentioned, already published structures were improved by this process. General guidelines were given for the crystal structure determination of very heavy compounds. When using Mo Kα radiation with uranium compounds, the proximity of its energy to the uranium L-edges causes a noticeable effect.

Synthesis and Crystal Structures of Novel Group 6B Metal Carbonyl Complexes with N‐(4‐methyl‐2‐pyridinyl)‐P,P‐diphenylphosphinous Amide Ligand

AbstractThe reaction of N‐(4‐methyl‐2‐pyridinyl)‐P,P‐diphenylphosphinous amide ligand 4‐Me‐C5H3N‐2‐NH(PPh2) (1) with M(CO)6 (M=Cr, Mo, W) in refluxing toluene afforded a mononuclear group VIB metal tetracarbonyls [M(CO)4{1‐κ2P,N}] (M=Cr(2), Mo(3), W(4)). Complexes 2–4 were characterized by multinuclear NMR (1H, 13C and 31P NMR) and IR spectroscopy, and their structures were also determined by single crystal X‐ray diffraction. 2 and 4 represent the first examples of structurally characterized complexes of such ligands with group 6B metal carbonyls.

Non-benzenoid N-aryl oxalamide: synthesis of troponyl-oxalamide peptides by Pd(II)-catalyzed C(sp3)-H functionalization of glycinamides.

Aryl oxalamides are constituents of various promising drug-like molecules. Their aryl groups are derived from the benzenoid aromatic moiety. However, non-benzenoid aromatic molecules, troponoids, are found in various bioactive natural products. It would be thought-provoking to explore non-benzenoid aryl oxalamide derivatives. This report describes the synthesis of N-troponyl-oxalamide peptides by Pd(II)-catalyzed C(sp3)-H functionalization of N-troponyl glycinate peptides. This is the first instance of β-hydride elimination at the palladium complex of N-troponyl glycinates that generates imine in situ, rendering the synthesis of oxalamides. Importantly, the crystal structures of representative oxalamide derivatives form distinctive foldameric structures, such as β-sheet type structures, owing to the presence of additional troponyl carbonyl groups. Hence, these non-benzenoid oxalamides are potential scaffolds for tuning the structure and function of N-troponyl peptides, which could provide innovative avenues of research in the development of emerging structural and functional peptides.

Unveiling the carbonation behavior of T-C3S and M-C3S: A comparative investigation

Numerous studies have investigated the carbonation process of tricalcium silicate (C3S). However, research on the carbonation of its different crystal forms remains relatively limited. This study explored the effects of accelerated carbonation on the performance and microstructure of T-C3S and M-C3S. The findings indicated that both T-C3S and M-C3S exhibited a rapid carbonation reaction rate during the initial 12 h, which subsequently declined gradually. The carbonation products of T-C3S and M-C3S primarily consisted of calcite, with T-C3S also containing a proportion of aragonite calcium carbonate. The decomposition peak temperature of calcium carbonate weight loss increased with prolonged carbonation time for both C3S crystal forms. Prismatic or cubic morphology calcite formed in T-C3S and M-C3S during the initial carbonation stages, leading to a denser microstructure. As the carbonation duration increased, the particle size of calcite also grew, displaying a more irregular morphology. Furthermore, needle-like or rod-like aragonite calcium carbonate was observed in T-C3S. T-C3S exhibited superior compressive strength compared to M-C3S at all stages of carbonation. Additionally, a relationship was established between compressive strength, calcium carbonate content, and CO2 uptake. This study provided evidence that the crystal structure of C3S not only influenced the rate of the carbonation reaction but also impacted the type and morphology of calcium carbonate products and the development of compressive strength.

Solid-State Reaction of Alkylamines with CO2 in Ambient Air.

This paper explores possible procedures to accelerate CO2 capture from ambient air by a crystalline alkylamine surfactant (octadecylamine), leading to the corresponding crystalline ammonium-carbamate. Conversion of the amine to the carbamate, in different conditions, is studied by four different techniques: WAXD, FTIR, TGA, and DSC. The WAXD study also gives relevant information on the crystal structures of both amine and derived carbamate. Kinetics of reactions of the crystalline amine are mainly studied by DSC scans, by evaluating melting enthalpies of residual amine. The kinetics of conversion of the amine in ambient CO2 is strongly accelerated by ball milling with full conversion achieved after only 4 h, while the reaction kinetics of amine powder simply exposed to ambient CO2 is complete only after nearly 103 h. A substantial increase in kinetics of the solid-state amine reaction with ambient CO2 can be also achieved by increasing the temperature up to 50 °C, i. e. at a temperature slightly lower than amine melting. However, the time for full conversion remains much higher than for room-temperature ball-milled amine (roughly 102 h vs 4 h). Hence, suitable ball-milling procedures can lead to complete and relatively fast conversion of the crystalline amine to the crystalline ammonium-carbamate, even with ambient CO2.

Effect of Mn2+ Doping and DDAB-Assisted Postpassivation on the Structural and Optical Properties of CsPb(Cl/Br)3 Halide Perovskite Nanocrystals.

Cesium lead halide perovskite (CsPbX3; X = Cl, Br, I) nanocrystals showing intense band-edge emission and high photoluminescence quantum yield are known to be a potential candidate for application in optoelectronic devices. However, controlling toxicity due to the presence of Pb2+ in lead-based halide perovskites is a major challenge for the environment that needs to be tackled cautiously. In this work, we have partially replaced Pb2+ with Mn2+ ions in the CsPb(Cl/Br)3 nanocrystals and investigated their impact on the structural and optical properties. The Rietveld refinement shows that CsPbCl2Br nanocrystals possess a cubic crystal structure with Pm3 ̅m space group, the Mn2+ doping results in the contraction of the unit cell. The CsPb(Cl/Br)3: Mn nanocrystals show a substantial change in the optical properties with an additional emission band at ~588 nm through a d-d transition, changing the emission color from blue to pink. Here, a didodecyldimethylammonium bromide (DDAB) ligand that triggers both anion and ligand exchange in the CsPb(Cl/Br)3: Mn nanocrystals have been used to regulate the exchange reaction and tune the emission color of halide perovskites by changing the peak position and the PL intensities of band-edge and Mn2+ defect states. We have also shown that oleic acid helps in the desorption of oleylamine capping from the CsPb(Cl/Br)3: Mn nanocrystal surfaces and DDAB, resulting in the substitution of Cl¯ with Br¯ as well as provides capping with shorter branched length ligand which led to increase in the overall PL intensity by many folds.

Crystal structure of the class A extended-spectrum β-lactamase CTX-M-96 in complex with relebactam at 1.03 Angstrom resolution.

The use of β-lactam/β-lactamase inhibitors constitutes an important strategy to counteract β-lactamases in multidrug-resistant (MDR) Gram-negative bacteria. Recent reports have described ceftazidime-/avibactam-resistant isolates producing CTX-M variants with different amino acid substitutions (e.g., P167S, L169Q, and S130G). Relebactam (REL) combined with imipenem has proved very effective against Enterobacterales producing ESBLs, serine-carbapenemases, and AmpCs. Herein, we evaluated the inhibitory efficacy of REL against CTX-M-96, a CTX-M-15-type variant. The CTX-M-96 structure was obtained in complex with REL at 1.03 Å resolution (PDB 8EHH). REL was covalently bound to the S70-Oγ atom upon cleavage of the C7-N6 bond. Compared with apo CTX-M-96, binding of REL forces a slight displacement of the deacylating water inwards the active site (0.81 Å), making the E166 and N170 side chains shift to create a proper hydrogen bonding network. Binding of REL also disturbs the hydrophobic patch formed by Y105, P107, and Y129, likely due to the piperidine ring of REL that creates clashes with these residues. Also, a remarkable change in the positioning of the N104 sidechain is also affected by the piperidine ring. Therefore, differences in the kinetic behavior of REL against class A β-lactamases seem to rely, at least in part, on differences in the residues being involved in the association and stabilization of the inhibitor before hydrolysis. Our data provide the biochemical and structural basis for REL effectiveness against CTX-M-producing Gram-negative pathogens and essential details for further DBO design. Imipenem/REL remains an important choice for dealing with isolates co-producing CTX-M with other β-lactamases.

The Peculiar Molecular [(IF5)6(HF2)4]4− Anion of the Compound K4[(IF5)6(HF2)4

AbstractK4[(IF5)6(HF2)4] was obtained from the reaction of K[HF2] with liquid IF5. The compound was analyzed by single crystal and powder X‐ray diffraction, Raman spectroscopy, and quantum‐chemical calculations. It contains the largest molecular IF5/HF2− complex anion known so far. Surprisingly, the crystal structure of the A4B compound can be related to the Hg4Pt structure type.

High ionic conductivity materials Li3YBr6 and Li3LaBr6 for solid-state batteries: first-principles calculations

High ionic conductivity solid-state electrolytes are essential for powerful solid-state lithium-ion batteries. With density functional theory andab initiomolecular dynamics simulations, we investigated the crystal structures of Li3YBr6and Li3LaBr6. The lowest energy configurations with uniform distribution of lithium ions were identified. Both materials have wide electrochemical stability windows (ESW): 2.64 V and 2.57 V, respectively. The experimental ESW for Li3YBr6is 2.50 V. Through extrapolating various temperature diffusion results, the conductivity of Li3YBr6was obtained at room temperature, approximately 3.9 mS cm-1, which is comparable to the experimental value 3.3 mS cm-1. Li3LaBr6has a higher conductivity, a 100% increase compared with Li3YBr6. The activation energies of Li3YBr6and Li3LaBr6through the Arrhenius plot are 0.26 eV and 0.24 eV, respectively, which is also close to the experimental value of 0.30 eV for Li3YBr6. This research explored high ionic conductivity halide materials and will contribute to developing solid-state lithium-ion batteries.

Mn-inlaid antiphase boundaries in perovskite structure

Improvements in the polarization of environmentally-friendly perovskite ferroelectrics have proved to be a challenging task in order to replace the toxic Pb-based counterparts. In contrast to common methods by complex chemical composition designs, we have formed Mn-inlaid antiphase boundaries in Mn-doped (K,Na)NbO3 thin films using pulsed laser deposition method. Here, we observed that mono- or bi-atomic layer of Mn has been identified to inlay along the antiphase boundaries to balance the charges originated from the deficiency of alkali ions and to induce the strain in the KNN films. Thus, rectangular saturated polarization-electric field hysteresis loops have been achieved, with a significantly improved twice remanent polarization of 114 μC/cm2 with an applied electric field of 606 kV/cm, which can be comparable to that of the typical Pb-based thin films. Moreover, we directly see the Mn occupation at the A-site of KNN perovskite structure using atomic-scale microstructure and composition analysis. The Mn-inlaid antiphase boundary can further enrich the understanding of perovskite crystal structure and give more possibilities for the design and optimization of perovskite materials.

Exploring Phase Transition and Structural Complexity in the Mixed Cation Uranium Oxide CaUNb2O8.

The structures and high-temperature phase transition of CaUNb2O8 were studied in situ using synchrotron X-ray and neutron powder diffraction. Rietveld refinements provided an accurate description of the crystal structures of both the monoclinic fergusonite-type I2/b structure observed at room temperature and the tetragonal scheelite-type I41/a structure found at high temperatures. Bond valence sum analysis showed Nb5+ to be octahedrally coordinated in the monoclinic fergusonite-type structure, akin to other ANbO4 materials. Rietveld analysis of the variable temperature data allowed for the determination of accurate unit cell parameters and atomic coordinates, as well as revealing a reversible phase transition around ∼750 °C. The Nb-O bond distances display anomalous behavior, with a discontinuity in the longer Nb-O(1') distance coinciding with the phase transition suggestive of a reconstructive phase transition. Mode analysis identified the Γ2+ mode as the primary mode that drives the phase transition; this is linearly coupled to the induced spontaneous strain within the monoclinic fergusonite-type structure. Analysis of the temperature dependence of the Nb(z) positional parameter, as well as of the ϵ1-ϵ2 and ϵ6 strain parameters, showed that the phase transition is not strictly second order, with the critical exponent β ≠ 1/2. This study demonstrates the complex structural features of mixed cation metal oxides at elevated temperatures.

Structural and Mutational Analyses of Trehalose Synthase from Deinococcus radiodurans Reveal the Interconversion of Maltose-Trehalose Mechanism.

Trehalose synthase (TreS) catalyzes the reversible interconversion of maltose to trehalose, playing a vital role in trehalose production. Understanding the catalytic mechanism of TreS is crucial for optimizing the enzyme activity and enhancing its suitability for industrial applications. Here, we report the crystal structures of both the wild type and the E324D mutant of Deinococcus radiodurans trehalose synthase in complex with the trehalose analogue, validoxylamine A. By employing structure-guided mutagenesis, we identified N253, E320, and E324 as crucial residues within the +1 subsite for isomerase activity. Based on these complex structures, we propose the catalytic mechanism underlying the reversible interconversion of maltose to trehalose. These findings significantly advance our comprehension of the reaction mechanism of TreS.

Adjusting the Energy Profile for CH-O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations.

The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.

All "Roads" Lead to Rocksalt Structure.

Rocksalt is the most common crystal structure among binary compounds. Moreover, no long-lived, metastable polymorphs are observed in compounds with the rocksalt ground state. We investigate the absence of polymorphism via first-principles random structure sampling and transformation kinetics modeling of three rocksalt compounds: MgO, TaC, and PbTe. Random structure sampling reveals that for all three systems the rocksalt basin of attraction covers much more of configuration space than any other, making it statistically the most significant structure. The kinetics modeling shows that virtually all other relevant structures, including most of the 457 known A1B1 prototypes, transform rapidly to rocksalt, making it the only option at ambient conditions. These results explain the absence of polymorphism in binary rocksalts, answer why rocksalt is the structure of choice for high-entropy ceramics and disordered ternary nitrides, and help understand/predict metastable states in crystalline solids more generally.

The role of defect charge, crystal chemistry, and crystal structure on positron lifetimes of vacancies in oxides

Density functional theory based positron lifetime (PL) calculations for cation and oxygen monovacancies in a range of oxides-hematite, magnetite, hercynite, and alumina-have been conducted to compare the impact of defect chemistry and crystal structure on the predicted lifetimes. The role of defect charge state has also been examined. A comparison across the same type of crystalline structure but different composition shows that oxygen vacancies only induce a slight increase in the positron-electron overlap and thus barely modify the PL as compared to the bulk. A much more substantial increase of PL is observed for cation monovacancies, regardless of crystal structure or the elemental nature of the vacancy, which we ascribe to an enhanced localization of charge density around the vacant site. The structural and compositional richness of the oxide leads to longer defect PLs, with defected hercynite exhibiting the longest PLs. The charge state of cation monovacancies modifies only by a small percentage the positron localization, relegating to secondary importance the metal defect's oxidation state in modifying the lifetime of positrons within vacancy traps.

1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) as target for anti Toxoplasma gondii agents: crystal structure, biochemical characterisation and biological evaluation of inhibitors.

Toxoplasma gondii is a widely distributed apicomplexan parasite causing toxoplasmosis, a critical health issue for immunocompromised individuals and for congenitally infected foetuses. Current treatment options are limited in number and associated with severe side effects. Thus, novel anti-toxoplasma agents need to be identified and developed. 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) is considered the rate-limiting enzyme in the non-mevalonate pathway for the biosynthesis of the isoprenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the parasite, and has been previously investigated for its key role as a novel drug target in some species, encompassing Plasmodia, Mycobacteria and E. coli. In this study, we present the first crystal structure of T. gondii DXR (TgDXR) in a tertiary complex with the inhibitor fosmidomycin and the cofactor NADPH in dimeric conformation at 2.5 Å resolution revealing the inhibitor binding mode. In addition, we biologically characterize α-phenyl-ß-thia and -oxa reverse fosmidomycin analogues and show that some derivatives are strong inhibitors of TgDXR which also, in contrast to fosmidomycin, inhibit the growth of T. gondii in vitro. Here, ((3,4-dichlorophenyl)((2-(hydroxy(methyl)amino)-2-oxoethyl)thio)methyl)phosphonic acid was identified as the most potent anti T. gondii compound. These findings will enable the future design and development of more potent anti-toxoplasma DXR inhibitors.

Negative thermal expansion in hexagonal VF3 predicted by first-principles calculation

Abstract Searching negative thermal expansion (NTE) materials is challenging. Herein, hexagonal VF3 is predicted as a new NTE material for the first time. VF3 displays NTE property in the temperature range from 0 to 380 K, and the minimum NTE coefficient(α) is approximately -4.68×10-6 K-1 at 120 K. The NTE mechanism was ascribed to the vibrations of F atom with larger atomic displacement parameters, which dominates the negative Grüneisen parameters. The difference of minimum NTE coefficient between VF3 and TiF3 might be caused by their different chemical bond strength between Ti-F and V-F. This research provides a deeper understanding between NTE and crystal structure.

Preparation and Properties of Hydroxyapatite-Ti composite Thin Films by Co-sputtering Method for Biocompatibility Applications

Abstract In this paper, we report on enhancing the biocompatibility properties of Hydroxyapatite-Titanium (HA-Ti) thin films fabricated using the co-sputtering method. By adjusting the HA/Ti ratio through varying the sputtering power of Ti, we obtained HA-Ti thin films with different crystal structures, morphologies, and hydrophilic properties. HA-Ti thin films sputtered at different titanium powers of 80, 100, 120, 140, and 160 W will obtain thin films with larger grain sizes and poorer crystallinity, respectively. However, their hydrophilic properties increase as the contact angle decreases from 78 to 20 degrees. In vitro BHK cell tests indicated that the HA-Ti thin film had excellent biocompatibility. Therefore, this material is suitable for biological applications and has significant potential in medical implant technology.

Electro-optical effect of unpolarized light modulation in homeoplanar structures of ferroelectric and ferrielectric liquid crystals

A clearly expressed effect of unpolarized light electro-optical modulation by homeoplanar structures of a smectic C* ferroelectric liquid crystal (FLC) and a ferrielectric liquid crystal (FerriLC) was discovered and investigated for the first time to our knowledge. This effect of electrically controlled light scattering is insensitive to the applied voltage sign, as for polymer-dispersed nematic liquid crystals (PDLCs), but the electro-optical modulation frequency reaches the kilohertz range. Occurrence conditions and essential features of the effect, as well as its physical origin, are discussed.