Stacking Structure of Vaterite Revealed by Atomic Imaging and Diffraction Analysis.

Anhydrous calcium carbonate crystals exist as three polymorphs: calcite, aragonite, and vaterite. Although vaterite is a metastable phase rarely found in the geological environment, it is intriguing that various biominerals are composed of vaterite. The processes of stable vaterite formation in biological systems cannot be understood without elucidating the nature of vaterite. The crystal structure of vaterite has been discussed for nearly a century but is still an open question. Here we propose the actual structure of vaterite by combining atomic imaging and diffraction analysis with simulations of disordered stacking sequences. Vaterite basically appears as layers of hexagonal calcium planes and carbonate (CO3 2-)-containing sheets stacked with +60°, -60°, or 180° rotations from the underlying layer. However, equivalent carbonate positions in alternating layers are forbidden, and four-layer stacking in which the fourth layer rotates 180° relative to the first layer are predominant, forming an orthogonal reciprocal lattice in diffraction patterns. These stacking characteristics replicate the intensity distribution in the electron and X-ray diffraction patterns. This study has almost completely elucidated the crystal structure and stacking sequence of vaterite. Our findings provide insights into the thermodynamic stability of vaterite, which facilitates comprehension of the biomineralization processes and growth dynamics of calcium carbonate.

A Strategy Based on "Ambident Anthracene" for the Synthesis of Higher-Order Iptycenes.

An efficient method for the synthesis of higher-order iptycenes using an "ambident anthracene" building block is presented. For that purpose, an iterative elongation strategy involving the ring-opening of an endoxide to give a highly reactive anthranoxide, followed by a Diels-Alder reaction with an aryne was used. The method systematically provides higher-order iptycenes, including trideciptycene, which is currently the iptycene with the longest chain to have been synthesized. X-ray crystallography revealed interesting structures in which solvent molecules fill the cavities of these iptycenes, thus creating a "honeycomb" structure with the solvent molecules arranged in tubular spaces.

Self-Assembled Molecular Complexes of 1,10-Phenanthroline and 2-Aminobenzimidazoles: Synthesis, Structure Investigations, and Cytotoxic Properties.

Three new molecular complexes (phen)3(2-amino-Bz)2(H+)(BF4-)·3H2O 5, (phen)3(2-amino-5(6)-methyl-Bz)2(H+)(BF4-)·H2O 6, and (phen)(1-methyl-2-amino-Bz)(H+)(BF4-) 7, were prepared by self-assembly of 1,10-phenanthroline (phen) and various substituted 2-aminobenzimidazoles. Confirmation of their structures was established through spectroscopic methods and elemental analysis. The X-ray diffraction analysis revealed that the crystal structure of 7 is stabilized by the formation of hydrogen bonds and short contacts. In addition, the molecular geometry and electron structure of molecules 5 and 6 were theoretically evaluated using density functional theory (DFT) methods. According to the DFT B3LYP/6-311+G* calculations, the protonated benzimidazole (Bz) units act as NH hydrogen bond donors, binding two phenanthrolines and a BF4- ion. Non-protonated Bz unit form hydrogen bonds with the N-atoms of a third molecule phen. The molecular assembly is held together by π-π stacking between benzimidazole and phenanthroline rings, allowing for N-atoms to associate with water molecules. The complexes were tested in vitro for their tumor cell growth inhibitory effects on prostate (PC3), breast (MDA-MB-231 and MCF-7), and cervical (HeLa) cancer cell lines using MTT-dye reduction assay. The in vitro cytotoxicity analysis and spectrophotometric investigation in the presence of ct-DNA, showed that self-assembled molecules 5-7 are promising DNA-binding anticancer agents warranting further in-depth exploration.

Preparation and characterization of microcrystalline cellulose from rice bran.

BACKGROUND: Rice bran, a by-product of rice processing, has not been fully utilized except for the small amount used for raising animals. The raw material source requirements of microcrystalline cellulose are becoming increasingly extensive. However, the characteristics of preparing microcrystalline cellulose from rice bran have not been reported, which limits the application of rice bran. RESULTS: Microcrystalline cellulose was obtained from rice bran by alkali treatment, delignification, bleaching and acid hydrolysis. The morphology, particle size distribution, degree of polymerization, crystallinity, and thermal stability of rice bran microcrystalline cellulose were analyzed. The chemical compositions, scanning electron microscopy and Fourier-transform infrared analysis for rice bran microcrystalline cellulose showed that the lignin and hemicellulose were successfully removed from the rice bran fiber matrix. The morphology of rice bran microcrystalline cellulose was shown to be of a short rod-shaped porous structure with an average diameter of 65.3 µm. The polymerization degree of rice bran microcrystalline cellulose was 150. The X-ray diffraction pattern of rice bran microcrystalline cellulose showed the characteristic peak of natural cellulose (type I), and its crystallization index was 71%. The rice bran microcrystalline cellulose may be used in biological composites with temperatures between 150 °C and 250 °C. CONCLUSION: These results suggest the feasibility of using rice bran as a low-price source of microcrystalline cellulose. © 2024 Society of Chemical Industry.

Structural Analysis and Intrinsic Enzyme Mimicking Activities of Ligand-Free PtAg Nanoalloys.

Nanozymes are nanomaterials with biocatalytic properties under physiological conditions and are one class of artificial enzymes to overcome the high cost and low stability of natural enzymes. However, surface ligands on nanomaterials will decrease the catalytic activity of the nanozymes by blocking the active sites. To address this limitation, ligand-free PtAg nanoclusters (NCs) are synthesized and applied as nanozymes for various enzyme-mimicking reactions. By taking advantage of the mutual interaction of zeolitic imidazolate frameworks (ZIF-8) and Pt precursors, a good dispersion of PtAg bimetal NCs with a diameter of 1.78 ± 0.1 nm is achieved with ZIF-8 as a template. The incorporation of PtAgNCs in the voids of ZIF-8 is confirmed with structural analysis using the atomic pair-distribution function and powder X-ray diffraction. Importantly, the PtAgNCs present good catalytic activity for various enzyme-mimicking reactions, including peroxidase-/catalase- and oxidase-like reactions. Further, this work compares the catalytic activity between PtAg NCs and PtAg nanoparticles with different compositions and finds that these two nanozymes present a converse dependency of Ag-loading on their activity. This study contributes to the field of nanozymes and presents a potential option to prepare ligand-free bimetal biocatalysts with sizes in the nanocluster regime.

Comparative study of calcification in human choroid plexus, pineal gland, and habenula.

Choroid plexus, pineal gland, and habenula tend to accumulate physiologic calcifications (concrements) over a lifetime. However, until now the composition and causes of the intracranial calcifications remain unclear. The detailed analysis of concrements has been done by us using X-ray diffraction analysis (XRD), X-ray diffraction topography (XRDT), micro-CT, X-ray phase-contrast tomography (XPCT), as well as histology and immunohistochemistry (IHC). By combining physical (XRD) and biochemical (IHC) methods, we identified inorganic (hydroxyapatite) and organic (vimentin) components of the concrements. Via XPCT, XRDT, histological, and IHC methods, we assessed the structure of concrements within their appropriate tissue environment in both two and three dimensions. The study found that hydroxyapatite was a major component of all calcified depositions. It should be noted, however, that the concrements displayed distinctive characteristics corresponding to each specific structure of the brain. As a result, our study provides a basis for assessing the pathological and physiological changes that occur in brain structure containing calcifications.

Mechanism of D-Cycloserine Inhibition of D-Amino Acid Transaminase from Haliscomenobacter hydrossis.

D-cycloserine inhibits pyridoxal-5'-phosphate (PLP)-dependent enzymes. Inhibition effect depend on organization of the active site and mechanism of the catalyzed reaction. D-cycloserine interacts with the PLP form of the enzyme similarly to the substrate (amino acid), and this interaction is predominantly reversible. Several products of the interaction of PLP with D-cycloserine are known. For some enzymes formation of a stable aromatic product - hydroxyisoxazole-pyridoxamine-5'-phosphate at certain pH - leads to irreversible inhibition. The aim of this work was to study the mechanism of D-cycloserine inhibition of the PLP-dependent D-amino acid transaminase from Haliscomenobacter hydrossis. Spectral methods revealed several products of interaction of D-cycloserine with PLP in the active site of transaminase: oxime between PLP and ß-aminooxy-D-alanine, ketimine between pyridoxamine-5'-phosphate and cyclic form of D-cycloserine, and pyridoxamine-5'-phosphate. Formation of hydroxyisoxazole-pyridoxamine-5'-phosphate was not observed. 3D structure of the complex with D-cycloserine was obtained using X-ray diffraction analysis. In the active site of transaminase, a ketimine adduct between pyridoxamine-5'-phosphate and D-cycloserine in the cyclic form was found. Ketimine occupied two positions interacting with different active site residues via hydrogen bonds. Using kinetic and spectral methods we have shown that D-cycloserine inhibition is reversible, and activity of the inhibited transaminase from H. hydrossis could be restored by adding excess of keto substrate or excess of cofactor. The obtained results confirm reversibility of the inhibition by D-cycloserine and interconversion of various adducts of D-cycloserine and PLP.

N-N(+) Bond-Forming Intramolecular Cyclization of O-Tosyloxy ß-Aminopropioamidoximes and Ion Exchange Reaction for the Synthesis of 2-Aminospiropyrazolilammonium Chlorides and Hexafluorophosphates.

Our research area is related to the spiropyrazolinium-containingcompounds, which are insufficiently studied compared with pyrazoline-containing compounds. Nitrogen-containing azoniaspiromolecules have also been well studied. In drug design and other areas, they are a priori important structures, since rigid spirocyclic scaffolds with the reduced conformational entropy are able to organize a closely spaced area. Azoniaspirostructures are currently of wide practical interest as ionic liquids, current sources (membranes), structure-directing agents in organocatalysis, and in the synthesis of ordered ceramics. Our goal was the synthesis of 2-aminospiropyrazolilammonium chlorides and hexafluorophosphates. Our methodology is based on the tosylation of ß-aminopropioamidoximes with six-membered N-heterocycles (piperidine, morpholine, thiomorpholine, and phenylpiperazine) at the ß-position. 2-Aminospiropyrazolilammonium chlorides and hexafluorophosphates were obtained by the reaction of double ion substitution in the reaction of toluenesulfonates of 2-aminospiropyrazolinium compounds with an ethereal solution of HCl in ethanol and with ammonium hexafluorophosphate in ethanol in quantitative yields of 55-97%. The physicochemical characteristics of the synthesized compounds and their IR and NMR spectra are presented. The obtained salts were additionally characterized by the single-crystal XRD analysis. The presence of both axial and equatorial conformations of spirocations in solids was confirmed. 2-Aminospiropyrazolilammonium chlorides and hexafluorophosphates have weak in vitro antimicrobial activity on Gram-positive and Gram-negative bacterial lines.

Niobium Complexes Supported by Chalcogen-Bridged [OEO]-Type Bis(phenolate) Ligands (E = S, Se): Synthesis, Characterization, and Phenylacetylene Polymerization.

Trichloro niobium(V) complexes 3 and 4 with the sulfur- or selenium-bridged [OEO]-type bis(phenolate) ligands (E = S, Se) were synthesized and fully characterized on the basis of their NMR spectroscopic data and X-ray crystallographic analysis. In the crystalline state of 4, the [OSeO]-core of the ligand was coordinated to the niobium center in a fac-fashion. The corresponding tribenzyl niobium(V) complexes 5 and 6 were also prepared by the reactions of 3 and 4 with 3 equivalents of PhCH2MgCl in toluene. The X-ray diffraction analysis of 6 revealed that the distorted six-coordinated niobium center incorporated in the [OSeO]-type ligand took a mer-fashion, and one benzyl ligand was coordinated to the niobium center by η2-fashion. Complexes 5 and 6 were tested for the phenylacetylene polymerization that produced poly(phenylacetylene)s (PPAs), oligomers, and triphenylbenzenes (TPBs) depending on the chalcogen atom in the [OEO]-type ligand.

Aluminum Salen Complexes Modified with Unsaturated Alcohol: Synthesis, Characterization, and Their Activity towards Ring-Opening Polymerization of ε-Caprolactone and D,L-Lactide.

A highly efficient one-step approach to the macromonomer synthesis using modified aluminum complexes as catalysts of ring-opening polymerization (ROP) of ε-caprolactone and D,L-lactide was developed. The syntheses, structures, and catalytic activities of a wide range of aluminum salen complexes, 3a-c, functionalized with unsaturated alcohol (HO(CH2)4OCH=CH2) are reported. X-Ray diffraction studies revealed a tetragonal pyramidal structure for 3c. Among the complexes 3a-c, the highest activity in bulk ROP of ε-caprolactone and D,L-lactide was displayed by 3b, affording polyesters with controlled molecular weights at low monomer to initiator ratios (Mn up to 15,000 g mol-1), relatively high polydispersities (Ð~1.8) and high number-average functionalities (Fn up to 85%).

The Novel Chiral 2(5H)-Furanone Sulfones Possessing Terpene Moiety: Synthesis and Biological Activity.

Over the past decades, 2(5H)-furanone derivatives have been extensively studied because of their promising ability to prevent the biofilm formation by various pathogenic bacteria. Here, we report the synthesis of a series of optically active sulfur-containing 2(5H)-furanone derivatives and characterize their biological activity. Novel thioethers were obtained by an interaction of stereochemically pure 5-(l)-menthyloxy- or 5-(l)-bornyloxy-2(5H)-furanones with aromatic thiols under basic conditions. Subsequent thioethers oxidation by an excess of hydrogen peroxide in acetic acid resulted in the formation of the corresponding chiral 2(5H)-furanone sulfones. The structure of synthesized compounds was confirmed by IR and NMR spectroscopy, HRMS, and single crystal X-ray diffraction. The leading compound, 26, possessing the sulfonyl group and l-borneol moiety, exhibited the prominent activity against Staphylococcus aureus and Bacillus subtilis with MICs of 8 µg/mL. Furthermore, at concentrations of 0.4-0.5 µg/mL, the sulfone 26 increased two-fold the efficacy of aminoglycosides gentamicin and amikacin against S. aureus. The treatment of the model-infected skin wound in the rat with a combination of gentamicin and sulfone 26 speeded up the bacterial decontamination and improved the healing of the wound. The presented results provide valuable new insights into the chemistry of 2(5H)-furanone derivatives and associated biological activities.

Crystalline analysis of dental enamel by X-Ray diffraction on pediatric patients with chronic kidney disease.

This study aimed to analyze the crystalline structure of dental enamel in pediatric patients with chronic kidney disease (CKD) by X-ray diffraction (XRD). The six tested samples had a mineral composition similar to hydroxyapatite, according to sheet JCPDS(Joint Committee on Powder Diffraction Standards) card #09-0432, which is normally found in dentine, and presented a lower amount of whitlockites (Ca, Mg)3(PO4)2. Pattern phases showed an increase in organic matter and a decrease in inorganic matter. At an interval of approximately 2θ = 15.7° to 27.2°, amorphous organic matter corresponding to hydrated glucose was found. The hydroxyapatite patterns in this study differed from that of dental enamel found on permanent teeth.

Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis.

The interaction between the series of berberine derivatives 1-5 (NAX071, NAX120, NAX075, NAX077 and NAX079) and human telomeric G-quadruplexes (G4), which are able to inhibit the Telomerase enzyme's activity in malignant cells, was investigated. The derivatives bear a pyridine moiety connected by a hydrocarbon linker of varying length (n = 1-5, with n number of aliphatic carbon atoms) to the C13 position of the parent berberine. As for the G4s, both bimolecular 5'-TAGGGTTAGGGT-3' (Tel12) and monomolecular 5'-TAGGGTTAGGGTTAGGGTTAGGG-3' (Tel23) DNA oligonucleotides were considered. Spectrophotometric titrations, melting tests, X-ray diffraction solid state analysis and in silico molecular dynamics (MD) simulations were used to describe the different systems. The results were compared in search of structure-activity relationships. The analysis pointed out the formation of 1:1 complexes between Tel12 and all ligands, whereas both 1:1 and 2:1 ligand/G4 stoichiometries were found for the adduct formed by NAX071 (n = 1). Tel12, with tetrads free from the hindrance by the loop, showed a higher affinity. The details of the different binding geometries were discussed, highlighting the importance of H-bonds given by the berberine benzodioxole group and a correlation between the strength of binding and the hydrocarbon linker length. Theoretical (MD) and experimental (X-ray) structural studies evidence the possibility for the berberine core to interact with one or both G4 strands, depending on the constraints given by the linker length, thus affecting the G4 stabilization effect.

Synthesis, Structure and Photochemistry of Dibenzylidenecyclobutanones.

A series of symmetrical dibenzylidene derivatives of cyclobutanone were synthesized with the goal of studying the physicochemical properties of cross-conjugated dienones (ketocyanine dyes). The structures of the products were established and studied by X-ray diffraction and by NMR and electronic spectroscopy. All the products had E,E-geometry. The oxidation and reduction potentials of the dienones were determined by cyclic voltammetry. The potentials were shown to depend on the nature, position, and number of substituents in the benzene rings. A linear correlation was found between the difference of the electrochemical oxidation and reduction potentials and the energy of the long-wavelength absorption maximum. This correlation can be employed to analyze the properties of other compounds of this type. Quantum chemistry was used to explain the observed regularities in the electrochemistry, absorption, and fluorescence of the dyes. The results are in good agreement with the experimental redox potentials and spectroscopy data.

High-Temperature Spin Crossover in Iron(II) Complexes with 2,6-Bis(1H-imidazol-2-yl)pyridine.

Novel iron(II) coordination compounds containing a ligand 2,6-bis(1H-imidazol-2-yl)pyridine (L), having such a composition as [FeL2]SO4·0.5H2O, [FeL2]Br2·H2O, [FeL2](ReO4)2, [FeL2]B10H10∙H2O, [FeL2]B12H12∙1.5H2O had been synthesized and studied using UV-Vis (diffuse reflectance), infrared, extended X-ray absorption fine structure (EXAFS), and Mössbauer spectroscopy methods, as well as X-ray diffraction and static magnetic susceptibility methods. The analysis of the µeff(T) dependence in the temperature range of 80-600 K have shown that all the obtained complexes exhibit a high-temperature spin crossover 1A1 ↔ 5T2.

Granatripodins A-B, limonoids featuring a Tricyclo[3.3.1.02,8]nonane motif: Absolute configuration and agonistic effects on human pregnane-X-receptor.

Two unprecedented limonoids incorporating a sterically encumbered cyclopropane ring, named granatripodins A (1) and B (2), featuring the presence of a tricyclo[3.3.1.02,8]nonane motif, were obtained from seeds of the Thai Xylocarpus granatum. The planar structures and absolute configurations of these limonoids were unambiguously established by NMR investigations, TDDFT-ECD and DFT-NMR calculations, and single-crystal X-ray diffraction analysis (Cu Kα). Most notably, granatripodin A (1) exhibited agonistic effects on human pregnane-X-receptor at the concentration of 100.0 nM. The biosynthetic origins of these limonoids via a radical cascade reaction are proposed. This study exemplifies a universal approach for the stereochemical assignment of polycyclic compounds with a cyclopropane-embedded cage scaffold.

A Path to the Atomic-Resolution Structures of Prokaryotic and Eukaryotic Ribosomes.

Resolving first crystal structures of prokaryotic and eukaryotic ribosomes by our group has been based on the knowledge accumulated over the decades of studies, starting with the first electron microscopy images of the ribosome obtained by J. Pallade in 1955. In 1983, A. Spirin, then a Director of the Protein Research Institute of the USSR Academy of Sciences, initiated the first study aimed at solving the structure of ribosomes using X-ray structural analysis. In 1999, our group in collaboration with H. Noller published the first crystal structure of entire bacterial ribosome in a complex with its major functional ligands, such as messenger RNA and three transport RNAs at the A, P, and E sites. In 2011, our laboratory published the first atomic-resolution structure of eukaryotic ribosome solved by the X-ray diffraction analysis that confirmed the conserved nature of the main ribosomal functional components, such as the decoding and peptidyl transferase centers, was confirmed, and eukaryote-specific elements of the ribosome were described. Using X-ray structural analysis, we investigated general principles of protein biosynthesis inhibition in eukaryotic ribosomes, along with the mechanisms of antibiotic resistance. Structural differences between bacterial and eukaryotic ribosomes that determine the differences in their inhibition were established. These and subsequent atomic-resolution structures of the functional ribosome demonstrated for the first time the details of binding of messenger and transport RNAs, which was the first step towards understanding how the ribosome structure ultimately determines its functions.

Living-Cell Diffracted X-ray Tracking Analysis Confirmed Internal Salt Bridge Is Critical for Ligand-Induced Twisting Motion of Serotonin Receptors.

Serotonin receptors play important roles in neuronal excitation, emotion, platelet aggregation, and vasoconstriction. The serotonin receptor subtype 2A (5-HT2AR) is a Gq-coupled GPCR, which activate phospholipase C. Although the structures and functions of 5-HT2ARs have been well studied, little has been known about their real-time dynamics. In this study, we analyzed the intramolecular motion of the 5-HT2AR in living cells using the diffracted X-ray tracking (DXT) technique. The DXT is a very precise single-molecular analytical technique, which tracks diffraction spots from the gold nanocrystals labeled on the protein surface. Trajectory analysis provides insight into protein dynamics. The 5-HT2ARs were transiently expressed in HEK 293 cells, and the gold nanocrystals were attached to the N-terminal introduced FLAG-tag via anti-FLAG antibodies. The motions were recorded with a frame rate of 100 µs per frame. A lifetime filtering technique demonstrated that the unliganded receptors contain high mobility population with clockwise twisting. This rotation was, however, abolished by either a full agonist α-methylserotonin or an inverse agonist ketanserin. Mutation analysis revealed that the "ionic lock" between the DRY motif in the third transmembrane segment and a negatively charged residue of the sixth transmembrane segment is essential for the torsional motion at the N-terminus of the receptor.

Scattering of X-ray Ultrashort Pulses by Complex Polyatomic Structures.

The scattering of X-ray ultrashort pulses (USPs) is an important aspect of the diffraction analysis of matter using modern USP sources. The theoretical basis, which considers the specifics of the interaction of ultrashort pulses with complex polyatomic structures, is currently not well developed. In general, research is focused on the specifics of the interaction of ultrashort pulses with simple systems-these are atoms and simple molecules. In this work, a theory of scattering of X-ray ultrashort pulses by complex polyatomic structures is developed, considering the specifics of the interaction of ultrashort pulses with such a substance. The obtained expressions have a rather simple analytical form, which allows them to be used in diffraction analysis. As an example, it is shown that the obtained expressions can be used to study the structures of deoxyribonucleic (DNA) and ribonucleic (RNA) acids.

Cinnamal Sensing and Luminescence Color Tuning in a Series of Rare-Earth Metal-Organic Frameworks with Trans-1,4-cyclohexanedicarboxylate.

Three isostructural metal-organic frameworks ([Ln2(phen)2(NO3)2(chdc)2]·2DMF (Ln3+ = Y3+ for 1, Eu3+ for 2 or Tb3+ for 3; phen = 1,10-phenanthroline; H2chdc = trans-1,4-cyclohexanedicarboxylic acid) were synthesized and characterized. The compounds are based on a binuclear block {M2(phen)2(NO3)2(OOCR)4} assembled into a two-dime nsional square-grid network containing tetragonal channels with 26% total solvent-accessible volume. Yttrium (1)-, europium (2)- and terbium (3)-based structures emit in the blue, red and green regions, respectively, representing the basic colors of the standard RGB matrix. A doping of Eu3+ and/or Tb3+ centers into the Y3+-based phase led to mixed-metal compositions with tunable emission color and high quantum yields (QY) up to 84%. The bright luminescence of a suspension of microcrystalline 3 in DMF (QY = 78%) is effectively quenched by diluted cinnamaldehyde (cinnamal) solutions at millimolar concentrations, suggesting a convenient and analytically viable sensing method for this important chemical.