Crystal Structure Research Articles

Kenoargentotetrahedrite-(Zn), [Ag6]4+(Cu4Zn2)Sb4S12□, a new member of the tetrahedrite group from the Yindongpo Au deposit, China

Abstract. The new mineral kenoargentotetrahedrite-(Zn), [Ag6]4+(Cu4Zn2)Sb4S12□, was discovered at the Yindongpo Au deposit, Henan Province, China. It occurs as black metallic anhedral grains or equant crystals up to 40 µm in size. It is opaque in transmitted light and shows a greenish-grey colour in reflected light. Electron microprobe analysis for the studied material gave the empirical formula (on the basis of total cations being equal to 16 atoms per formula unit, apfu): M(2)(Ag3.75Cu2.25)Σ6M(1)[Cu3.90(Zn1.18Fe0.69Cd0.26)Σ2.13]Σ6.03X(3)(Sb3.69As0.27)Σ3.96S(1)S11.94 S(2)□. Kenoargentotetrahedrite-(Zn) is cubic, I4‾3m (no. 217), with a = 10.4624(4) Å, V= 1145.23(13) Å3, and Z= 2. The crystal structure has been refined to a final value of R1= 0.0247 on the basis of 274 independent reflections (Fo > 4σ (Fo)) by using single-crystal X-ray diffraction data. The seven strongest X-ray powder diffraction lines (d in Å (I) (hkl)) are the following: 3.010 (100) (222), 1.844 (30) (044), 2.606 (22) (004), 1.572 (15) (226), 2.046 (9) (134), 7.35 (6) (011), and 1.909 (5) (125). Kenoargentotetrahedrite-(Zn) is isostructural with other keno-member tetrahedrites with the [Ag6]4+ cluster. The structure refinement result confirms the coupling between the site occupancy factor of subvalent hexasilver clusters at the M(2) site and that of the vacancy at the S(2) site. This relationship further substantiates the charge balance substitution mechanism of S-deficiency tetrahedrites: 6M(2)Ag++S(2)S2-= M(2)[Ag6]4++S(2)□.

Powder X-ray diffraction of nintedanib esylate hemihydrate, (C31H33N5O4)(C2H5O3S)(H2O)0.5

The crystal structure of nintedanib esylate hemihydrate was refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Nintedanib esylate hemihydrate crystallizes in space group P-1 (#2) with a = 11.5137(1), b = 16.3208(4), c = 19.1780(5) Å, α = 69.0259(12), β = 84.4955(8), γ = 89.8319(6)°, V = 3347.57(3) Å3, and Z = 4 at 295 K. Hydrogen bonds are prominent in the crystal structure. The water molecule forms two medium-strength O–H⋯O hydrogen bonds to one of the esylate anions. The protonated nitrogen atom in each cation forms a N–H⋯O hydrogen bond to an esylate anion. The ring N–H groups form strong intramolecular N–H⋯O hydrogen bonds to carbonyl groups. The ring N–H groups form intramolecular N–H⋯O hydrogen bonds to esylate anions. Many C–H⋅⋅⋅O hydrogen bonds (and one C–H⋯N hydrogen bond), with aromatic C–H, methylene groups and methyl groups as donors, are present. The hydrogen bonding patterns of the two cations differ considerably. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®)

Trans-Dichloridobis(secnidazole-κN 3)copper(II)

The use of acetic acid (HOAc) in a reaction between CuCl2·2H2O and secnidazole, an active pharmaceutical ingredient useful in the treatment against a variety of anaerobic Gram-positive and Gram-negative bacteria, affords the title complex, [CuCl2(C7H11N3O3)2]. This compound was previously synthesized using ethanol as solvent, although its crystal structure was not reported [Betanzos-Lara et al. (2013). Inorg. Chim. Acta, 397, 94–100]. In the molecular complex, the Cu2+ cation is situated at an inversion centre and displays a square-planar coordination environment. There is a hydrogen-bonded framework based on intermolecular O—H...Cl interactions, characterized by H...Cl separations of 2.28 (4) Å and O—H...Cl angles of 175 (3)°. The resulting supramolecular network is based on R2 2 (18) ring motifs, forming chains in the [010] direction.

Integrated study of the structural and magnetic characteristics of Nd(Mn, Cr)0.5O3: exploring perovskite material

In this work, a perovskite material, Nd(Mn,Cr)0.5O3, is synthesized by a sol–gel chemical route method, and the structural and magnetic properties of the prepared samples were studied for a range of annealing temperatures. The variation of structural parameters against annealing temperatures is analyzed via Rietveld refinement, and it exhibits orthorhombic cubic geometry with non-monotonically increasing lattice parameters. lattice strain is due to canting in the Cr3+ and Mn3+ ions and the presence of strain is also confirmed by the shifting of XRD peaks towards a higher 2θ angle. The obtained Goldschmidt tolerance factor is 0.87, which confirms the stability of the perovskite structure. The magnetic properties of the prepared samples show the ferromagnetic transition temperature ranging from 86.5 K to 82.2 K due to super-exchange interaction between Cr3+ and Mn3+ ions via oxygen ions. The stability in crystal structure, lower value of strain, and ferromagnetic nature at low temperature for the samples annealed up to1000 °C may make this material applicable for magnetic data storage.

Stabilizing Bifurcated Hydrogen Bond in 8-Aminoquinoline Appended Peptides.

The hydrogen bonding interaction between an amide N-H and the amide N of the preceding residue is prevalent in proline-containing proteins and peptides. However, the N-H···N hydrogen bonding interaction is rare in non-prolyl natural peptides due to restricted dihedral angles. Herein, we stabilize this type of interaction in 8-aminoquinoline appended non-prolyl peptides through bifurcated N···H···N hydrogen bond. The 8-aminoquinoline-incorporated model peptides 2a-i were designed, synthesized, and the crystal structures of 2a-c and 2i were solved. Analysis of crystal data reveals that the amide N-H of aminoquinoline is involved in bifurcated hydrogen bonding interaction with the nitrogen of the preceding amino acid residue and the nitrogen in quinoline. Analysis of crystal packing, Hirshfeld surface and fingerprint plots confirms that the intermolecular O···H contacts significantly contribute to stabilizing bifurcated N···H···N hydrogen bonding interaction. Furthermore, NMR experiments and CD spectroscopy were conducted to examine the preferred conformation in solution, and the data corroborate with the crystal structure conformation.

Oxoborates of the ludwigite group: Natural and mineral-like compounds as prospective materials

Research subject. Natural oxoborates of the ludwigite group, including azoproite, ludwigite, and vonsenite. Their empirical formulas based on five oxygen atoms have the following form: azoproite (Mg1.81Fe2+0.19)∑2.00(Fe3+0.36Ti0.26Mg0.26Al0.12)∑1.00 O2(BO3), ludwigite (Mg1.69Fe2+0.30Mn2+0.01)Σ2.00(Fe3+0.90Al0.07Mg0.02Sn0.01)Σ1.00O2(BO3) and vonsenite (Fe2+1.86Mg0.13)∑1.99 (Fe3+0.92Mn2+0.05Sn4+0.02Al0.02)∑1.01O2(BO3). Aim. To establish the relationship between the composition, crystal structure, and thermal behavior (293–1373 K) of the minerals. Materials and methods. Ludwigite was collected at the Iten’yurginskoe tin skarn deposit; vonsenite was collected at the Titovskoe magnesium-skarn boron deposit; azoproite was collected at magnesian skarns of the Tazheran alkaline massif. The methods of single crystal X-ray diffraction, energy dispersive X-ray spectroscopy, high-temperature X-ray diffraction, Mössbauer spectroscopy, and thermal analysis were used. Results. Low-charge cations (Fe2+, Fe2.5+, Mg2+) tend to occupy the M(1)–M(3) sites, and high-charge cations (Fe3+, Al3+, Ti4+, Sn4+) generally occupy the M(4) site. Azoproite is characterized by the highest melting temperature Tm > 1650 K. Due to the low Fe2+ content, azoproite does not undergo solid-phase decomposition across the investigated temperature range. The melting point of ludwigite exceeds 1582 K, which is due to the high Mg content; as a result of the Fe2+ → Fe3+ oxidation, it gradually decomposes with the formation of hematite, warwickite, and magnetite. The temperatures of oxidation and solid-phase decomposition in the Fe2+-rich vonsenite are approximately 100 K lower than those in ludwigite. The melting point of vonsenite is 1571 K. All the minerals are characterized by a weak degree of thermal expansion anisotropy. The main contribution to the thermal expansion anisotropy is due to the preferred orientation of the [BO3]3– triangles. Conclusions. The thermal properties of the oxoborates depend on their chemical composition. It was established that Tm increases with an increase in the Mg and Ti4+ content, and decreases with an increase in the Fe2+ content. The Fe2+ → Fe3+ oxidation is observed when the FeO component in the minerals exceeds 10 wt %, which leads to the solid-phase decomposition starting at temperatures of about 500–600 K. The values of the 293KαV volume thermal expansion of ludwigite and azoproite are comparable, while the largest values were observed for vonsenite. This is associated with the largest average bond lengths, primarily those of <Fe2+–O>6.

Amine-free synthesis of high-silica ZSM-5 assisted with calcined silicalite-1 and ethanol with the investigation of mechanism

Amine-free synthesis of high silica ZSM-5 with high crystallinity and well-defined morphology was challenging. In this work, ZSM-5 with the fed silica-alumina ratio (SAR) of 100 was rapidly synthesized with the assistance of the calcined silicalite-1 seed and ethanol, and their crystal structures, morphology and microporous properties were characterized by XRD, SEM, FT-IR, ICP and N2 adsorption-desorption and so on. Firstly, the crystallization temperature was optimized between 140 and 180 °C at a certain alkalinity and ethanol content, and 160 °C was selected to not only provide high crystallization rate but also ensure the stability of high-silica skeleton. Secondly, the influences of the EtOH/SiO2 ratio, Na2O/SiO2 ratio and crystallization time on the crystallization of high-silica ZSM-5 were investigated at 160 °C. The results showed well-crystalline high-silica ZSM-5 could be synthesized within a wide range of the EtOH/SiO2 ratios (0.5–2.0) and the increase of ethanol content slightly inhibited the growth of ZSM-5 along b-axial of hexagonal prisms due to the preferential adsorption of excess ethanol on the {010} crystal plane and the formation of Si–O–C2H5; high alkalinity was favorable for the preparation of a small-sized and well-crystalline ZSM-5 due to the rapid depolymerization of calcined seed and the contribution of mass nucleation sites; meanwhile, excellent micropore characteristic of high-silica ZSM-5 further proved that the synthetic strategy of seed + ethanol was feasible. Finally, the synergistic action mechanism of calcined seed and ethanol for the synthesis of high-silica ZSM-5 was revealed that silicalite-1 with MFI structure unit combined with Na+(H2O/EtOH) with larger radius were very important for rapidly assembly of a large number of silica species into MFI framework.

CeO2 nanoparticles modified screen-printed carbon electrode: Electrochemical sensing platform for sulfite determination in water samples

In the present work, the CeO2 nanoparticles (CeO2 NPs) were prepared by hydrothermal method and the crystal structure and morphology analysis were studied by using a series of characterizations. Then, the screen-printed carbon electrode (SPCE) modified with CeO2 NPs was employed to develop a simple and novel sensor for sulfite determination in water samples. The CeO2 NPs/SPCE showed significant current response for sulfite oxidation. The use of the developed sensor with differential pulse voltammetry (DPV) method provides a wide linear range for sulfite determination (0.08–870.0 µM) with a low limit of detection (LOD) (0.023 µM). Finally, the results determination of sulfite in water samples showed good recoveries between 96.7% and 102.7% with a relative standard deviation (RSD) less than 3.6%.

Crystal Structure, Hirshfeld Surface, Vibrational Study, Optical Properties and Biological Activities of a Novel Hybrid Material 2-Methylpiperazine-1,4-Dium Tetrachlorocobaltate(II) based on DFT Calculation

Crystal Structure, Hirshfeld Surface, Vibrational Study, Optical Properties and Biological Activities of a Novel Hybrid Material 2-Methylpiperazine-1,4-Dium Tetrachlorocobaltate(II) based on DFT Calculation

Visualizing the Internal Nanocrystallinity of Calcite Due to Nonclassical Crystallization by 3D Coherent X-Ray Diffraction Imaging.

The internal crystallinity of calcite is investigated for samples synthesized using two approaches: precipitation from solution and the ammonium carbonate diffusion method. Scanning electron microscopy (SEM) analyses reveal that the calcite products precipitated using both approaches have a well-defined rhombohedron shape, consistent with the euhedral crystal habit of the mineral. The internal structure of these calcite crystals is characterized using Bragg coherent diffraction imaging (BCDI) to determine the 3D electron density and the atomic displacement field. BCDI reconstructions for crystals synthesized using the ammonium carbonate diffusion approach have the expected euhedral shape, with internal strain fields and few internal defects. In contrast, the crystals synthesized by precipitation from solution have very complex external shapes and defective internal structures, presenting null electron density regions and pronounced displacement field distributions. These heterogeneities are interpreted as multiple crystalline domains, created by a nonclassical crystallization mechanism, where smaller nanoparticles coalescence into the final euhedral particles. The combined use of SEM, X-ray diffraction (XRD), and BCDI allows for structurally differentiating calcite crystals grown with different approaches, opening new opportunities to understand how grain boundaries and internal defects alter calcite reactivity.

O vacancy-rich doped WO3/GF as a novel electrode for an aqueous DHAQ/ K4Fe(CN)6 redox flow battery

In this study, a graphite felt (GF) electrode was modified with N and S heteroatoms before being loaded with Ti-doped or Nb-doped WO3 to produce Ti-WO3/GF-N-S and Nb-WO3/GF-N-S electrodes. X-ray diffraction, scanning electron microscopy, and X-ray photoelectron spectroscopy were used to analyze the crystal structure, morphology, and elemental state of the modified GF electrodes and investigate the impact of nonmetallic and metallic element doping. The influence of metal doping on the electronic distribution of the oxide was determined using first-principle calculations. The electrochemical properties of the modified GF were studied using cyclic voltammetry, electrochemical impedance spectroscopy, and single-cell tests. The results showed that Ti or Nb doping changed the energy band structure, bond length, and bond angle in the WO3 crystal and formed O vacancies. The chemical properties of Ti and Nb resulted in different numbers of O vacancies for the two doped-WO3.The doping of N and S heteroatoms on the carbon fibres altered the O vacancy concentration of WO3. The synergism between the two doping methods accelerated electron transfer in the anthraquinone redox reaction. In addition, the N-containing functional groups provide lone-pair electrons, which accelerate electron transfer and anthraquinone adsorption. Therefore, compared to the pristine GF, the discharge capacities of the Ti-WO3/GF-N-S and Nb-h-WO3/GF-N-S graphite GF electrodes increased by 58 % and 41 %, respectively, and the Nb-h-WO3/GF-N-S graphite GF electrodes exhibited a good capacity retention rate. This study broadens the practical applications of aqueous anthraquinone redox flow batteries.

Evidence of disordered local structure of ZnO buffered MgB2 films via polarized extended X-ray absorption fine structure analysis

Herein, we investigated the mechanism by which the critical temperature (Tc) of a magnesium diboride (MgB2) superconductor is altered by the buffer layer. Zinc oxide (ZnO) layers with different thicknesses (28, 80, and 134 nm) were deposited epitaxially on a Hastelloy substrate beneath a ∼ 1 μm MgB2 film. To measure the local structural distortion of the boron plane, three different angle polarizations (0°, 45°, and 90° parallel to the ab-axis) on the Mg K-edge, extended X-ray absorption fine structure (EXAFS) measurements were performed. The EXAFS analyses revealed that the ZnO buffer layer caused the boron layer to disorient, leading to buckling between the Mg and B layers, which affected the charge transfer capability in the intra-layer structure. Furthermore, the uneven distribution of B atoms amid the surrounding Mg atoms resulted in an asymmetric crystal structure, which leads to Tc fluctuation. This study reveals the relationship between modifications made to the boron plane condition of MgB2 by the ZnO buffer layer and the superconducting Tc behavior of MgB2.

Paragenetic and geological setting of the Starra iron oxide copper–gold deposits, Mount Isa Inlier, Queensland, Australia: constraints on IOCG deposit models

The five Starra iron oxide copper–gold (IOCG) deposits, which are located in the Cloncurry district of the Mount Isa Inlier, NW Queensland, are hosted in a N-trending zone of deformed iron-rich metasedimentary rocks that are underlain by two mineralogically distinct mafic–intermediate meta-igneous rocks. Copper–Au mineralisation is subdivided into two stages—an early main stage that transitioned from a magnetite-dominated Cu substage comprising chalcopyrite, pyrite, biotite and chlorite, to a hematite–muscovite-bearing Cu–Au substage with chalcopyrite, bornite and rare chalcocite, as well as Au–Ag-tellurides and native Au. This second stage was followed by a subordinate but nonetheless important carbonate–quartz–barite vein stage with minor but locally high-grade Cu–Au mineralisation characterised by abundant chalcocite and bornite, minor native bismuth and wittichenite (Cu3BiS3), together with minor Au–Ag telluride minerals. Bornite in these carbonate–quartz–barite veins contains considerable amounts of Au (>10 ppm), which appears to be deported either as lattice substitution in the bornite crystal structure or as homogeneously distributed Au0 nanoparticles. An earlier, coarse-grained mafic intrusion was affected by early Na–Ca alteration, whereas a second mafic intrusion lacks evidence of Na–Ca alteration but was exposed to K–Fe alteration and subsequent mineralisation at Starra 222. Mushketovite (magnetite after specular hematite) is only observed in ironstone lodes proximal to the mafic–intermediate rocks. The close spatial and mineralogical associations of the mafic–intermediate bodies and the ironstone lodes point to a stronger link between magmatic activity and IOCG mineralisation than has previously been recognised at Starra. Remobilisation of gold by late-stage hydrothermal fluids aided by the relatively low fluid temperatures during the main pulse of Cu–Au mineralisation refined gold grades at Starra, making it a relatively gold-rich IOCG deposit. We show that the Cu–Au deposits of the Starra trend feature mineralogical and geochemical elements common to both Cloncurry IOCG deposits (e.g. abundant magnetite) and IOCG deposits of the Tennant Creek district (e.g. Au–Cu–Bi mineralisation; hematite–bornite–chalcocite assemblages), making them a unique and important member of this complex family of deposits.

Symmetry Reduction of Molecular Shape of Cationic Chromophores for High‐Performance Terahertz Generators

AbstractThe symmetry reduction of molecular shape of cationic chromophores as a design strategy to develop organic terahertz (THz) generators is used. Electron donating group (EDG) with an asymmetric shape is introduced into two types of cationic styryl‐quinolinium chromophores, leading to the development of several novel non‐centrosymmetric crystals with high macroscopic optical nonlinearity. In contrast, when an EDG with a symmetric shape is introduced, centrosymmetric crystal structure is obtained in all investigated crystals. For THz wave generation, crystals based on asymmetrically shaped EDG exhibit several optimal crystal characteristics, including a plate‐shape morphology, a large size, and an in‐plane polar axis. Furthermore, over the entire range of molecular phonon vibrations, 0.5–4 THz, the steric hindrance group in the asymmetrically shaped EDG has a strong influence on the suppression of THz phonon vibrations, leading to a low THz absorption coefficient. The crystals based on asymmetrically shaped EDG generate an ≈40 times stronger THz electric field than the inorganic ZnTe crystal and very broad THz spectra, extending up to 16 THz. Thus, the symmetry reduction of the molecular shape of cationic chromophores through the introduction of an asymmetrically shaped EDG is an effective design approach for the development of novel organic THz crystals.

Major structural types in inorganic chemistry and mineralogy: New data

Research subject. Structural types with different stoichiometric correlations between chemical elements. Aim. To analyze the prevalence of structural types with different stoichiometric correlations between chemical elements, such as simple substances with binary compounds, triple compounds with stoichiometry ABX3, triple compounds with stoichiometry AB2X4. Key points. The analysis was conducted using the databases of inorganic compounds ICSD (Inorganic Crystal Structure Database) and PCD (Pearson’s Crystal Data). The number of entries with the most typical structural types for 2013 and 2023 are determined. Their classifications in various databases for different years are given. The ranks of structural types for minerals and inorganic compounds are analyzed. The minerals crystallized in all the considered structural types are indicated according to the 2023 ISCD data, sampling only by the number of minerals registered in IMA (International Mineralogical Association – Commission on New Minerals, Nomenclature and Classification) for March 2023. The Russian names of minerals are presented in accordance with the database WWW-MINCRIST for the minerals crystallizing in all the structural types under consideration. Conclusions. The most probable causes for the realization of each stoichiometric correlation in various structural types are determined. The prevalence of certain structural types among inorganic compounds and minerals, as well as the underlying reasons, are discussed based on the principles of crystal chemistry.

Structural basis of chorismate isomerization by Arabidopsis ISOCHORISMATE SYNTHASE1.

Salicylic acid (SA) plays a crucial role in plant defense against biotrophic and semi-biotrophic pathogens. In Arabidopsis (Arabidopsis thaliana), isochorismate synthase 1 (AtICS1) is a key enzyme for the pathogen-induced biosynthesis of SA via catalytic conversion of chorismate into isochorismate, an essential precursor for SA synthesis. Despite the extensive knowledge of ICS1-related menaquinone, siderophore, tryptophan (MST) enzymes in bacteria, the structural mechanisms for substrate binding and catalysis in plant isochorismate synthase (ICS) enzymes are unknown. This study reveals that plant ICS enzymes catalyze the isomerization of chorismate through a magnesium-dependent mechanism, with AtICS1 exhibiting the most substantial catalytic activity. Additionally, we present high-resolution crystal structures of apo AtICS1 and its complex with chorismate, offering detailed insights into the mechanisms of substrate recognition and catalysis. Importantly, our investigation indicates the existence of a potential substrate entrance channel and a gating mechanism regulating substrate into the catalytic site. Structural comparisons of AtICS1 with MST enzymes suggest a shared structural framework with conserved gating and catalytic mechanisms. This work provides valuable insights into the structural and regulatory mechanisms governing substrate delivery and catalysis in AtICS1, as well as other plant ICS enzymes.

Perovskite materials advance the potent sensor exploration

AbstractPerovskite materials with unique crystal structure have developed rapidly in recent years owing to their special physical and chemical properties, such as high light absorption and extraordinary electrocatalytic properties. Metal halide perovskites are quite attractive in various fields because of their simple manufacturing process, adjustable band gap, good charge transfer performance, and high theoretical photoelectric conversion efficiency. Therefore, perovskite oxides mixed with metal elements become ideal samples for studying the surface and catalytic performance of catalysts. In this review, various metal perovskites are clearly classified and introduced according to the corresponding synthesis methods, including hydrothermal method, sol–gel method, and high‐temperature solid phase, as well as coprecipitation. The excellent properties of perovskite make it extensively used in nanotechnology, chemistry, environmental protection, and material science, especially in solar cells and sensors. In particular, the nanosized perovskite materials are becoming more and more popular in sensors, which was reviewed in detail here. Most importantly, the design of electrochemical sensors using perovskite nanomaterials with low detection limit and high sensitivity will bring new insight into the detection of biomolecules. Both challenges and prospects of metal perovskites were discussed for promoting the development of biosensors in the end.

Functional Construction of a Novel Lanthanide MOF for Efficient Ratio Luminescence Detection of Ethanol Vapor

AbstractIt is necessary to develop excellent sensors for volatile organic compounds (VOCs) detection from the perspective of environmental protection and human health. Luminescent lanthanide metal‐organic frameworks (MOFs) have many advantages such as porosity, luminescence, and structural controllability, making them very suitable as luminescent sensing materials. Based on a functional oriented strategy, novel Ln‐MOFs are successfully constructed and their structure and properties are characterized in detail. A series of vapor luminescence sensing tests have shown that Eu/Tb doped L1‐Eu0.1/Tb0.9 not only exhibits high selectivity for alcohols, especially ethanol vapor, but also has high sensitivity and extremely low detection limit (9.76 mg L−1). To the knowledge, there are no reports on ratio luminescence sensors based on Ln‐MOFs for ethanol vapor, especially those with such excellent performance. Crystal structure determination demonstrates that ethanol binds to the framework through multiple hydrogen bonding interactions, altering the energy transfer efficiency between Tb3+ and Eu3+ to achieve ratio luminescence detection. In addition, L1‐Eu0.1/Tb0.9 has good repeatability, the prepared thin film sensing material also demonstrates the advantages of portability and processability. This work can provide some experience for the development of VOCs sensing materials with better performance.

Phosphorus–nitrogen compounds: part 75—design, synthesis, stereogenic and conformational properties of chiral dispiro(N/N)cyclotriphosphazenes: structural analysis and photophysical and bioactivity studies

AbstractMultiheterocyclic inorganic–organic hybrid phosphazenes have robust inorganic ring systems with the stabilities of the phosphorus nitrogen skeleton and many different substituents bonded to the P atoms. In present study, unsymmetrical dispirocyclotriphosphazenes were prepared due to their potential to depict steric hindrance and electronic rearrangement in creating permanent chirality for certain conformational and configurational isomers. These isomers may have an effect on DNA bindings and activitiy against selected fungi and bacteria, remarkably. Herein, tetrachlorocyclotriphosphazenes (1 and 2) were reacted with 9-ethyl-N-methyl-3-carbazolyl-1,2-diaminoethane (3), 9-ethyl-N-ethyl-3-carbazolyl-1,2-diaminoethane (4) and 9-ethyl-N-methyl-3-carbazolyl-1,3-diaminopropane (5) to give the new unsymmetrical cis/trans-dispirocyclotriphosphazenes, [(ClBz/BzSpiro-6)R1(N3P3)(CzSpiro-n)R2]Cl2 (Cz: Carbazolyl; R1:Me R2:Me or Et; n = 5 or 6; trans 6a–11a and cis 6b–11b). Characterizations, chiralities, and photophysical and biological properties of the new compounds were examined. The molecular and crystal structures of cis-6b, cis-7b, trans-9a, cis-9b, trans-10a and cis-10b were determined by single crystal X-ray crystallography. The chiralities of these compounds with unsymmetrical spiro-architectures were confirmed by X-ray crystallography. These results were further proven by 31P NMR data recorded with the addition of a chiral solvent (CSA). Additionally, circular dichroism (CD) spectra also supported the results. Photophysical measurements indicate that these compounds show emission with lifetimes of approximately 5.6–5.9 ns. In addition, the bioactivities of some isomers were found to be different and quite high against some bacterial and yeast strains. Trans-8a was very active against B. cereus (MBC = 78.1 µM), while cis-6b, trans-9a and cis-9b were very active against the pathogenic yeast C. albicans (MFC = 156.3 µM). Graphical abstract

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses.

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.