Crystallographic Analysis Research Articles

Hierarchical Multi‐Component Self‐Assembly Involving Alkali and Lanthanide(III) Metal Ions and Water Soluble Sulfonated Calix[4]arene

AbstractSolid state structural studies of three supramolecular coordination complexes establish the formation of hetero‐bimetallic two‐ and three‐dimensional ensembles involving sulfonated calix[4]arene, and sodium ions and low nuclearity lanthanide(III) ions. The interplay of components is altered in response to the addition of different auxiliary molecules during crystallisation which is associated with significant changes in the metal coordination environments and overall molecular packing, as established in comparing the structures of complexes of similar cell dimensions with those available in the literature. The sulfonated calixarene form a common self‐assembly array despite different lanthanides being incorporated, as an isostructural series of complexes. Crystallographic analysis shows a continually decreasing trend in the lanthanide–oxygen bond length as the lanthanide atomic number increases. As smaller molecules are incorporated to the hetero‐bimetallic calixarene system, the self‐assembly and the metal coordination environment are perturbed.

Local Crystallographic Texture of Alpha Quartz in Silicified Wood (Late Triassic, Madagascar)

Compositional and anatomical studies of silicified wood have been carried out extensively all around the world. The classification of silicified wood as such deals with all the forms and phases of silica that come under its umbrella. One such class of silicified wood is fossil wood with a high content of quartz, and there are very limited mentions of this category of fossilized wood. The examined wood belongs to gymnosperm and comes from the Upper Triassic deposits of Madagascar. A fresh approach to such samples is adopted by studying the crystallographic texture of the fossil wood to understand the orientation of the crystals replacing the organic matter within the sample. This work focuses on crystallographic texture analysis based on pole figures measured by X-ray diffraction. The intensity of the pole density maxima on the pole figures measured on the heartwood surface part of the analyzed samples is higher than that on the sapwood. This affirms that the crystallographic texture is sharper at the heartwood part compared to the sapwood. The X-ray tomography study, conducted to understand the difference in mineral distribution within the sample, reveals a greater X-ray absorbing phase on the sapwood of both samples. This is due to the concentration of iron compounds, which both replace the remaining conductive structures of the wood and fill the cavities inside them. We believe that this research on silicified wood is the first research work that encompasses crystallographic texture analysis with pole figures, an approach not previously undertaken in similar studies. We hope that our research can be useful in understanding the processes of replacement of organic matter by minerals.

Synthesis, Chiroptical Properties, and Absolute Configuration Determination of Phenyl‐4‐pyridyl‐2,5‐dipyrimidinylmethane

Phenyl‐4‐pyridyl‐2,5‐dipyrimidinylmethane (1) has been synthesized in five steps from 5‐methylpyrimidine. The structural feature of 1 is the symmetry elements with respect to the 180º rotation of the aryl group along the central C‐C bonds. Due to this structural feature, the compound 1 is expected the good crystallinity despite of the asymmetric molecular structure. The optical resolution of 1 was achieved by high performance liquid chromatography using chiral stationary phase (chiral HPLC). The circular dichroism (CD) spectra of the two fractions showed opposite signs. As expected, the X‐ray crystallographic analysis was successfully performed for both the racemic and enantiomerically pure crystals of compound 1, with the nitrogen atoms being unambiguously assigned in both cases. It was concluded the first‐eluted fraction in chiral HPLC was determined to be S configuration both by the CD calculation for reproducing the experimental CD spectrum and by the anomalous diffraction of X‐ray crystallographic analysis of enantiomerically pure 1.

Brønsted Acid‐Stibine Oxide Complexes as Organocatalysts for the Activation of Alkenes

AbstractVarious hydroxystibonium salts were synthesized via the one‐pot oxidation/salt formation of a series of triarylstibines. The properties of the ortho‐substituents on the aryl groups were elucidated via X‐ray crystallographic analysis and computational studies. Moreover, the catalytic reactivity of the hydroxystibonium salts with alkenes was investigated, and the involvement of a radical species is proposed based on the results of mechanistic studies.

Dicyclopenta[4,3,2,1‐cde:4',3',2',1'‐pqr]‐peri‐tetracene: Synthesis and An Example of Annulene‐Within‐An‐Annulene Aromaticity in Different Redox States

We report a robust strategy for tuning the electronic structure and chemical stability of π‐conjugated polycyclic hydrocarbons (PHs). By fusing two cyclopentadienyl rings in the peri‐tetracene bay regions, we introduce antiaromatic character into the π‐system, leading to unique photophysical and electronic properties. A stable mesityl‐substituted dicyclopenta‐peri‐tetracene derivative was synthesized through stepwise formylation/intramolecular cyclization at the bay regions of the dihydro peri‐tetracene precursor, followed by oxidative dehydrogenation. This compound features an open‐shell singlet diradical ground state, global antiaromaticity, exceptional stability under ambient conditions, and amphoteric redox behavior with a small energy gap. Its dication also possesses an open‐shell singlet ground state, and its structure was identified by X‐ray crystallographic analysis, revealing a unique [14]annulene‐within‐[22]annulene global aromatic structure. In contrast, the dianion exhibits a closed‐shell singlet ground state. This work provides valuable insights for designing and synthesizing novel open‐shell PHs with tunable electronic structures and remarkable stability.

Mutant-selective AKT inhibition through lysine targeting and neo-zinc chelation.

Somatic alterations in the oncogenic kinase AKT1 have been identified in a broad spectrum of solid tumours. The most common AKT1 alteration replaces Glu17 with Lys (E17K) in the regulatory pleckstrin homology domain1, resulting in constitutive membrane localization and activation of oncogenic signalling. In clinical studies, pan-AKT inhibitors have been found to cause dose-limiting hyperglycaemia2-6, which has motivated the search for mutant-selective inhibitors. We exploited the E17K mutation to design allosteric, lysine-targeted salicylaldehyde inhibitors with selectivity for AKT1 (E17K) over wild-type AKT paralogues, a major challenge given the presence of three conserved lysines near the allosteric site. Crystallographic analysis of the covalent inhibitor complex unexpectedly revealed an adventitious tetrahedral zinc ion that coordinates two proximal cysteines in the kinase activation loop while simultaneously engaging the E17K-imine conjugate. The salicylaldimine complex with AKT1 (E17K), but not that with wild-type AKT1, recruits endogenous Zn2+ in cells, resulting in sustained inhibition. A salicylaldehyde-based inhibitor was efficacious in AKT1 (E17K) tumour xenograft models at doses that did not induce hyperglycaemia. Our study demonstrates the potential to achieve exquisite residence-time-based selectivity for AKT1 (E17K) by targeting the mutant lysine together with Zn2+ chelation by the resulting salicylaldimine adduct.

Unveiling the Monoclinic Phase in CsPbBr3-xClx Perovskite Crystals, Phase Transition Suppression and High Energy Resolution γ-Ray Detection.

All-inorganic CsPbBr3 and CsPbCl3 perovskites are promising materials for high-performance solar cells and advanced radiation detection technologies with high stability. Here we report that CsPbBr3-xClx (x = 0-3) crystals exhibit eutectoid behavior for the melting points and phase transition temperatures. The well-known halide perovskite cubic phase transition temperature shifts near room temperature (∼37 °C for CsPbBr2Cl). We conducted an extensive crystallographic analysis on single crystals of 7 different compositions, including the end members CsPbBr3 and CsPbCl3. Contrary to previous beliefs, we discovered they exhibit a monoclinic structure with space group symmetry P21/m at room temperature, rather than the orthorhombic Pnma. This new structural model is more precise and features a unit cell volume that is four times larger than that of the orthorhombic model. From high-quality single crystals of CsPbBr2Cl, grown by the Bridgman method, we constructed γ-ray detectors achieving an energy resolution of 7.2% at 200 V for 57Co radiation. Thermally stimulated current spectroscopy of the CsPbBr2Cl samples revealed that the defect densities in crystals from different regions of the ingot were relatively uniform, with values of ∼4.72 × 1012 and ∼5.09 × 1012 cm-3. These findings indicate that low deep-level defect densities can be achieved that are consistent with the notable performance of the CsPbBr2Cl perovskite as a high-energy γ radiation detector.

Dicyclopenta[4,3,2,1-cde:4',3',2',1'-pqr]-peri-tetracene: Synthesis and An Example of Annulene-Within-An-Annulene Aromaticity in Different Redox States.

We report a robust strategy for tuning the electronic structure and chemical stability of π-conjugated polycyclic hydrocarbons (PHs). By fusing two cyclopentadienyl rings in the peri-tetracene bay regions, we introduce antiaromatic character into the π-system, leading to unique photophysical and electronic properties. A stable mesityl-substituted dicyclopenta-peri-tetracene derivative was synthesized through stepwise formylation/intramolecular cyclization at the bay regions of the dihydro peri-tetracene precursor, followed by oxidative dehydrogenation. This compound features an open-shell singlet diradical ground state, global antiaromaticity, exceptional stability under ambient conditions, and amphoteric redox behavior with a small energy gap. Its dication also possesses an open-shell singlet ground state, and its structure was identified by X-ray crystallographic analysis, revealing a unique [14]annulene-within-[22]annulene global aromatic structure. In contrast, the dianion exhibits a closed-shell singlet ground state. This work provides valuable insights for designing and synthesizing novel open-shell PHs with tunable electronic structures and remarkable stability.

CYP3A4-mediated metabolism of artemisinin to 10β-hydroxyartemisinin with comparable anti-malarial potency.

The most widely used anti-malarial drug artemisinin (ART) is metabolized extensively, but the therapeutic capacity of its major metabolite remains unknown. Whether the major metabolite of ART (ART-M) contributes to its antiplasmodial potency was investigated in this study. The metabolite identification and enzyme phenotyping of ART were performed using human liver microsomes (HLMs). The stereostructure of the major metabolite ART-M was elucidated by spectroscopic and X-ray crystallographic analysis. The anti-malarial activity of ART-M against two reference Plasmodium strains (Pf3D7 and PfDd2) was evaluated. The pharmacokinetic profiles of ART and its metabolite ART-M were investigated in healthy Chinese subjects after a recommended two-day oral dose of ART plus piperaquine. Pharmacodynamic parameters based on minimum inhibitory concentration (MIC50) and free plasma concentration were employed to evaluate the therapeutic potency of ART-M, including fAUC0-t/MIC50, fCmax/MIC50 and T > MIC50. A major metabolite 10β-hydroxyartemisinin (ART-M) was found for ART in human, and CYP3A4/3A5 was the major enzymes responsible for ART 10β-hydroxylation. Compared with ART (MIC50, 10.1nM against Pf3D7), weaker antiplasmodial activity was found for ART-M (MIC50, 61.4nM against Pf3D7). However, a 3.5-fold higher maximal free plasma concentration was achieved for ART-M (fCmax, 180.0nM vs. 51.8nM for ART). ART-M displayed comparable antiplasmodial potency to ART, in terms of fAUC0-t/MIC50 (12.5h), fCmax/MIC50 (2.8) and T > MIC50 (5h). The major metabolite 10β-hydroxyartemisinin contributes to the antiplasmodial efficacy of ART, which should be considered when evaluation of ART dosing regimens and/or clinical outcomes.

Thuwalamides A–E: polychlorinated amides from the marine sponge Lamellodysidea herbacea collected from the Saudi Arabian Red Sea

Thuwalamides A–E (1, 3, 5, 6 and 8), previously undescribed polychlorinated amides, along with ten previously reported related compounds (2, 4, 7 and 9–15), were isolated from the organic extract of the marine sponge Lamellodysidea herbacea (Keller), collected off the village of Thuwal in the Red Sea at Saudi Arabia. The structures of the isolated compounds have been determined through extensive analysis of their NMR and MS data, while their absolute stereochemistry was unequivocally established via single crystal X-ray diffraction. Additionally, the absolute stereochemistry of the previously reported compounds 2 and 4, whose configuration was not determined, has also been established using single-crystal X-ray crystallographic analysis. The antibacterial activity of compounds 1–15 was evaluated against Escherichia coli and Staphylococcus aureus. Among them, compound 14 displayed activity against S. aureus comparable to vancomycin that was used as a positive control with a MIC value of 4 μg/mL.

Incorporation of phenylcarbonyl groups in the sidechain: A tool to induce ordered assembly of peptides on surfaces.

The possibility of introducing various functionalities on peptides with relative ease allows them to be used for molecular applications. However, oligopeptides prepared entirely from proteinogenic amino acids seldom assemble as ordered structures on surfaces. Therefore, sidechain modifications of peptides that can increase the intermolecular interactions without altering the constitution of a given peptide become an attractive route to self-assembling them on surfaces. We find that replacing phenylalanine residues with unusual amino acids that have phenylcarbonyl sidechains in oligopeptides increases the formation of ordered self-assembly on a highly ordered pyrolytic graphite surface. Peptides containing the modified amino acids provided extended long-range ordered assemblies, while the analogous peptides containing phenylalanine residues failed to form long-range assemblies. X-ray crystallographic analysis of the bulk structures of these peptides and the analogous peptides containing phenylalanine residues reveal that such modifications do not alter the secondary structure in crystals. It also reveals that the secondary hydrogen bonding interaction through phenylcarbonyl sidechains facilitates extended growth of the peptides on graphite.

Structural analysis and theoretical studies of 2-(2-chlorobenzylidene) malononitrile (CS) “a riot controlling agent”

In solvent methanol, malononitrile and 2-chlorobenzaldehyde were stirred in the presence of base piperidine to synthesise the target chemical 2-(2-chlorobenzylidene) malononitrile (CS). The crystal structure of the target compound C10H5ClN2 has been elucidated through X-ray crystallographic analysis. It crystallises in the monoclinic crystal system within the P21 space group, containing four molecules per asymmetric unit. The unit cell dimensions are a = 3.8825(3) Å, b = 21.0202(18) Å, c = 21.3481(18) Å, and β = 95.096(4)°. The phenyl and malononitrile groups, which make up the molecular components, are each planar but slanted towards one another at a dihedral angle of 12.7° (4). Besides this, target molecule is also stabilized by hydrogen bonding, halogen bonding and π stacking interactions. Solid-state structure has been analysed through Hirshfeld surface analysis, including the evaluation of the different energy frameworks, indicating that the molecular sheets are primarily formed by hydrogen bonds and halogen bonds and the stabilization is dominated via the electrostatic energy contribution. Fingerprint plots were carried out to study the relative contribution of noncovalent interactions in the target compound CS. Further, the density functional theory calculations were employed using B3LYP hybrid functional with 6-311++G level basic set to optimize the structural coordinates in gas phase and in different solvents (chloroform, water, and methanol). The chemically active regions of the target compound were identified by the analysis of molecular electrostatic potential surface. Further, from PASS analysis and literature reports, molecular docking of title compounds was carried out with human transient receptor potential ankyrin 1 ion channel (hTRPA1) (PDB-ID 6PQO). ΔGb (docking energy) and inhibition constant was calculated to be −7.53 kcal/mol and 3.33 μM respectively, with the target ion channel.

Three Metal Complex‐Decorated Halobismuthates: Syntheses, Structures, Semiconducting Behaviors and Theoretical Investigations

AbstractEmploying metal complex cations as the structural modifiers, three new numbers of hybrid halobismuthates family, namely [NH4][Co(phen)3]BiI6 (phen=1,10‐phenanthroline; 1), [Zn(phen)2Br][Bi(phen)Br4] ⋅ H2O (2) and [Cu(2,2′‐bipy)2Br][Cu(2,2′‐bipy)2Bi2Br9] ⋅ H2O (2,2′‐bipy=2,2′‐bipyridine; 3) have been solvothermally constructed and structurally characterized. X‐ray crystallography analyses show that all compounds characteristic of abundant weak interactions feature the discrete anionic motifs. The obtained hybrid materials possess the semiconducting nature, with the visible light responding optical band gaps of 2.13–2.71 eV. Under the alternating light irradiation, they exhibit excellent photoelectric switching properties, whose photocurrent densities (0.85, 0.24, and 0.43 μA/cm2 for compounds 1–3, respectively) compare well with some high‐performance halobismuthate competitors. Further theoretical calculations of compound 1 reveal that the photosensitive [Co(phen)3]2+ cations contribute greatly to the bottom of conduction bands (CBs) and the top of valence bands (VBs), which may be the important reason for its excellent photoelectric behavior. The analyses of Hirshfeld surface, thermal stability, and X‐ray photoelectron spectroscopy were also discussed detailedly in this paper.

Structural, Antioxidant, and Protein/DNA-Binding Properties of Sulfate-Coordinated Ni(II) Complex with Pyridoxal-Semicarbazone (PLSC) Ligand

The pyridoxal-semicarbazone (PLSC) ligand and its transition metal complexes have shown significant biological activity. In this contribution, a novel nickel(II)-PLSC complex, [Ni(PLSC)(SO4)(H2O)2], was obtained, and its structure was determined by X-ray crystallographic analysis, FTIR, and UV-VIS spectroscopy. The sulfate ion is directly coordinated to the central metal ion. The intermolecular stabilization interactions were examined using Hirshfeld surface analysis. The crystal structure was optimized by a B3LYP functional using two pseudopotentials for nickel(II) (LanL2DZ and def2-TZVP) together with a 6-311++G(d,p) basis set for non-metallic atoms. The experimental and theoretical bond lengths and angles were compared, and the appropriate level of theory was determined. The stabilization interactions within the coordination sphere were investigated by the Quantum Theory of Atoms in Molecules (QTAIM). The antioxidant activity towards hydroxyl and ascorbyl radicals was measured by EPR spectroscopy. The interactions between Human Serum Albumin (HSA) and the complex were examined by spectrofluorimetric titration and a molecular docking study. The mechanism of binding to DNA was analyzed by complex fluorescence quenching, potassium iodide quenching, and ethidium bromide displacement studies in conjunction with molecular docking simulations.

Two-Dimensional X-Ray Diffraction (2D-XRD) and Micro-Computed Tomography (Micro-CT) Characterization of Additively Manufactured 316L Stainless Steel

In-depth quality assessment of 3D-printed parts is vital in determining their overall characteristics. This study focuses on the use of 2D X-Ray diffraction (2D-XRD) and X-Ray micro-computed tomography (micro-CT) techniques to evaluate the crystallography and internal defects of 316L SS parts fabricated by the powder-based direct energy deposition (DED) technique. The test samples were printed in a controlled argon environment with variable laser power and print speeds, using a customized deposition pattern to achieve a high-density print (>99%). Multiple features, including hardness, elastic modulus, porosity, crystallographic orientation, and grain morphology and size were evaluated as a function of print parameters. Micro-CT was used for in-depth internal defect analysis, revealing lack-of-fusion and gas-induced (keyhole) pores and no observable micro-cracks or inclusions in most of the printed body. Some porosity was found mostly concentrated in the initial layers of print and decreased along the build direction. 2D-XRD was used for phase analysis and grain size determination. The phase analysis revealed single phase γ-austenitic FCC phase without any detectable presence of the δ-ferrite phase. A close correlation was found between Electron Backscatter Diffraction (EBSD) and 2D-XRD results on the average size distribution and the crystallographic orientation of grains in the sample. This work demonstrates the fast and reliable as-printed crystallography analysis using 2D-XRD compared to the EBSD technique, with potential for in-line integration.

Beautoide A, an Anti-Osteoclastogenic Sterol from Beauveria sp. NBUF147 Associated with an Irciniidae Sponge from the Marine Mesophotic Zone.

Mesophotic coral ecosystems (MCEs), located at depths ranging from 30-150 m, host some of the most diverse yet least explored marine bioresources, particularly significant for the discovery of new bioactive molecules. The fungus Beauveria sp. NBUF147, associated with an Irciniidae sponge from the mesophotic zone at a depth of 82 m, underwent chemical investigation that led to the identification of one new sterol, beautoide A (1), and one reported sterol, 3β,5α,9α-trihydroxy-(22E,24R)-ergosta-7,22-dien-6-one (2). Their structures were determined from analysis of spectroscopic data and X-ray crystallography. Evaluation of biological activity in prednisolone-induced osteoporotic zebrafish showed that 1 was anti-osteoclastogenic in vivo at 3.0 μM.

Highly Strained, Fully π‐Conjugated Porphyrin Cyclophanes: Template‐free Synthesis and Global Aromaticity

Porphyrin‐based nanohoops, nanorings, and cages with fully π‐conjugated structures are highly sought after, but their synthesis remains challenging. Herein, we report the template‐free synthesis of a highly strained, bithiophene‐bridged porphyrin cyclophane (1) from a porphyrin quinone via a stereoselective nucleophilic addition followed by intermolecular Yamamoto coupling strategy. X‐ray crystallographic analyses of 1 and its dication 12+ reveal significantly distorted cyclophane‐like geometries, with calculated strain energies of 51.2 and 80.7 kcal/mol, respectively. While the neutral compound 1 exhibits localized aromaticity, the dication 12+ is globally aromatic, with the porphyrin unit displaying weak antiaromaticity. Additionally, the dication 12+ undergoes nucleophilic addition with chloride, relieving strain. This work presents a novel synthetic strategy for highly strained, fully π‐conjugated systems with intriguing electronic properties and chemical reactivity.

Highly Strained, Fully π-Conjugated Porphyrin Cyclophanes: Template-free Synthesis and Global Aromaticity.

Porphyrin-based nanohoops, nanorings, and cages with fully π-conjugated structures are highly sought after, but their synthesis remains challenging. Herein, we report the template-free synthesis of a highly strained, bithiophene-bridged porphyrin cyclophane (1) from a porphyrin quinone via a stereoselective nucleophilic addition followed by intermolecular Yamamoto coupling strategy. X-ray crystallographic analyses of 1 and its dication 12+ reveal significantly distorted cyclophane-like geometries, with calculated strain energies of 51.2 and 80.7 kcal/mol, respectively. While the neutral compound 1 exhibits localized aromaticity, the dication 12+ is globally aromatic, with the porphyrin unit displaying weak antiaromaticity. Additionally, the dication 12+ undergoes nucleophilic addition with chloride, relieving strain. This work presents a novel synthetic strategy for highly strained, fully π-conjugated systems with intriguing electronic properties and chemical reactivity.

Aza‐Diarylethenes Undergoing Both Photochemically and Thermally Reversible Electrocyclic Reactions

AbstractExploring novel molecular photoswitches plays a crucial role in the field of photo‐functional materials chemistry. In this study, we synthesized aza‐diarylethenes with benzothiophene‐S,S‐dioxide as a part of the hexatriene structure and investigated their photochromic properties. Unlike previously reported aza‐diarylethenes, which exhibit fast thermally reversible photochromism, the compounds synthesized here exhibited pseudo‐photochemically reversible photochromism. Due to their thermal stability, we successfully isolated the colored isomer. X‐ray crystallographic analysis revealed for the first time that the colored isomer adopts a closed‐ring structure with a bond between carbon and nitrogen atoms. Remarkably, these aza‐diarylethenes exhibited not only photochemical ring‐closing and ring‐opening reactions but also thermal ring‐closing and ring‐opening reactions, driven by a thermal equilibrium between the open‐ and closed‐ring isomers. This behavior, unprecedented for common diarylethenes, was elucidated through kinetic analysis, revealing an energy‐level diagram for the thermal equilibrium between these isomers. Furthermore, 1H NMR spectroscopy revealed that both photochemically and thermally generated closed‐ring isomers adopt the same molecular structure, which was well explained based on the reaction mechanism of photochemical and thermal ring‐closing reactions. These findings not only advance the field of aza‐diarylethenes but also inspire future research in the development of new photoswitches.

Substrate recognition by the 4-hydroxytryptamine kinase PsiK in psilocybin biosynthesis.

Psilocybin, the natural hallucinogen from Psilocybe (magic) mushrooms, is a highly promising drug candidate for the treatment of depression and several other mental health conditions. Biosynthesis of psilocybin from the amino acid l-tryptophan involves four strictly sequential modifications. The third of these, ATP-dependent phosphorylation of the intermediate 4-hydroxytryptamine, is catalysed by PsiK. Here we present a crystallographic analysis and a structure-based mutagenesis study of this kinase, providing insight into its mode of substrate recognition. The results of our work will support future bioengineering efforts aimed at generating variants of psilocybin with enhanced therapeutic properties.