Crystals Of Complex Research Articles

Revealing protein structures: crystallization of protein-ligand complexes - co-crystallization and crystalsoaking.

Protein crystallogenesis represents a key step in X-ray crystallography studies that employ co-crystallization and ligand soaking for investigating ligand binding to proteins. Co-crystallization is a method that enables the precise determination of binding positions, although it necessitates a significant degree of optimization. The utilization of microseeding can facilitate a reduction in sample requirements and accelerate the co-crystallization process. Ligand soaking is the preferred method due to its simplicity; however, it requires careful control of soaking conditions to ensure the successful integration of the ligands. This research protocol details the procedures for co-crystallization and soaking to achieve protein-ligand complex formation, which is essential for advancing drug discovery. Additionally, a simple protocol for demonstrating soaking for educational purposes is described.

A dual-channel fluorescent probe based on salamo-Cu(II) complex for sensitive detection of S2- in river and tap water

A new double-salamo-type tetranuclear copper complex [Cu4(L)2](ClO4)2.2CH2Cl2 was designed and prepared, in which the metal atoms in the complex crystals have two different coordination systems, forming a symmetric structure as a whole. As a complex probe molecule, the addition of S2- in solution can achieve a red shift in the fluorescence spectrum, revealing bright green fluorescence, colorimetric and fluorescent dual-channel specific recognition ability and excellent anti-interference ability. The probe can be used to detect S2- by adding acidic and alkaline solutions to adjust the pH of the system for several cycles, which is suitable for ion recognition in most organisms and environments under pH conditions. The working mechanism of S2-recognition by Cu–ZTS was determined to be a synergistic action of ESIPT effect and ICT effect by correlation spectroscopy experiments, HR-MS and XPS tests, and this conclusion was subsequently further verified using theoretical calculations. Finally, the probe molecule showed good practical application value, and the portable test strips were prepared to qualitatively detect the ions, and by testing four different water samples, it was shown that the quantitative recognition of S2- could be realized almost without interference in real water samples. It proves that the coordination probe molecule has good prospects for practical application.

Photoluminescent Lanthanide(III) Complexes Based on 2-[((4-Chlorophenyl)amino)methylene]-5,5-dimethylcyclohexane-1,3-dione

Five coordination compounds of the general formula [LnL2(NO3)3]n (Ln3+ = Eu (I), Sm (II), Tb(III), Dy (IV), and Gd (V)) are synthesized from 2-[((4-chlorophenyl)amino)methylene]-5,5-dimethylcyclohexane-1,3-dione (L). The crystal structures of the ligand and complex III are determined by X-ray diffraction (XRD) of single crystals (CIF files CCDC nos. 2298715 (L) and 2298716 (III)). Complex III is polymeric due to the bidentate-bridging coordination of the ligand by the oxygen atoms of the cyclohexanedione fragment, and the coordination number of the central atom is ten. According to the phase XRD data, all synthesized polycrystalline compounds are isostructural to the single crystals of complex III. The photoluminescence properties of the ligand and coordination compounds in the polycrystalline state are studied. The energy transfer from the ligand to lanthanide(III) ion is shown to proceed via the “antenna” mechanism in the case of the europium(III), samarium(III), and terbium(III) compounds. Among the series of the complexes, the highest quantum yield is observed for compound I (21.9%), and the sensibilization efficiency of the europium(III) complex is 43.5%.

Crystal structure of bis-(μ2-5-nona-noylquinolin-8-olato)bis-[aqua-dichlorido-indium(III)

Crystallization of 5-nona-noyl-8-hy-droxy-quinoline in the presence of InCl3 in aceto-nitrile yields a dinuclear InIII complex crystallizing in the space group P. In this complex, [In2(C18H22NO2)2Cl4(H2O)2], each indium ion is sixfold coordinated by two chloride ions, one water mol-ecule and two 8-quinolino-late ions. The crystal of the title complex is composed of two-dimensional supra-molecular aggregates, resulting from the linkage of the Owater-H⋯O=C and Owater-H⋯Cl hydrogen bonds as well as bifurcated Carene-H⋯Cl contacts.

DNA/BSA Binding and Antimicrobial Properties of Biguanide-Cu(II) Complexes.

The biguanide Cu(II) complexes [Cu(L1-4)2](ClO4)2 were synthesized and spectroscopic/analytical techniques were used to clarify their structures. Single crystals of complex [Cu(L4)2](ClO4)2 was obtained and its definite structure was determined by single crystal X-ray diffraction study. The complexes [Cu(L1-4)2](ClO4)2 were screened for their FSds-DNA interactions by using UV-Vis absorption and fluorescence spectroscopies. The complexes [Cu(L2)2](ClO4)2 and [Cu(L3)2](ClO4)2 were shown to exhibit higher affinity for binding DNA. Examining the EB-DNA interaction, it is believed that the complexes interact with DNA through a groove binding mechanism. The interaction of complexes with BSA were observed through the quenching of the fluorescence emission. Complexes [Cu(L2)2](ClO4)2 and [Cu(L3)2](ClO4)2 show moderate binding affinity to BSA through a static mode. Additionally, the Cu(II) complexes were screened for their antibacterial activities against various bacterial strains. Complexes showed potential antimicrobial activity against Salmonella typhimurium, Bacillus cereus, Salmonella typhimurium and S. aureus.

Investigating the Mechanism of Triboluminescence: Insights from Structural and Electrostatic Characterization of Copper Thiocyanate Complexes.

Triboluminescence is a phenomenon in which light is generated through mechanical stress; it has emerging applications in stress-sensing devices. Although the prevailing mechanistic model indicates that light emits from charge separation and recombination in fracture planes arising from polar structures, its application in designing triboluminescent materials remains limited owing to numerous exceptions. This study provides insights into the essential requirements for triboluminescence by investigating the structural and electrostatic properties of fractured crystals of copper thiocyanate complexes. The examined fracture plane indicated that charge pairs (which are essential for light emission) form when intermolecular interactions are disrupted during fracturing. On the basis of the nature of these charges, we successfully suppressed triboluminescence by inhibiting the formation of intermolecular interactions disrupted in the examined complexes. Furthermore, we induced its re-emergence by creating an alternative fracture plane through controlled manipulation of the molecular network. This demonstrative deactivation and reactivation of triboluminescence underscores the critical role of intermolecular disruption in generating charge pairs, a prerequisite for triboluminescence.

Experimental and DFT perspectives: exploring spectral, linear and nonlinear optical properties of p-nitrophenol complex crystal for NLO applications

Experimental and DFT perspectives: exploring spectral, linear and nonlinear optical properties of p-nitrophenol complex crystal for NLO applications

Shaped ionic wood for enhanced phase change performance

Wood with a porous structure is the best carrier for phase change energy storage materials, which can effectively prevent material leakage during thermal cycling and ensure its shaping effect. In this work, natural poplar wood was treated with delignification and then oxidized by TEMPO as a thermal energy storage matrix. Then, it was immersed in a solution of ethanol as the solvent, polyethylene glycol (PEG) and calcium chloride as the solutes, obtaining phase change energy storage ionic wood (DTW-PCMs). The results showed that the phase change energy storage material PEG-CaCl2 was successfully impregnated into the pore structure of wood; calcium chloride was effectively combined with –COOH in TEMPO oxidized wood for intermediate bonds and formed white complex crystals with PEG2000. The maximum absorption rate and differential scanning calorimetry (DSC) test results showed that TEMPO-oxidized poplar had a maximum absorption rate of 95.26% for PEG2000-CaCl2. Additionally, TEMPO-oxidized poplar exhibited good phase transition performance and suitable phase change temperature. The latent heat of phase transition was 86.96 J/g. Thus, the novel DTW-PCMs displayed a high potential application in the field of thermal energy storage and temperature regulation.

Kinetics study and fragility of (Cu50Zr43Al7)98Y2 bulk metallic glass

Crystallization transformation kinetics and fragility of (Cu50Zr43Al7)98Y2 bulk metallic glass (BMG) were investigated at non-isothermal and isothermal conditions by differential scanning calorimetry. Activation energies for the BMG were calculated for the glass transition, onset crystallization, and crystallization peak using various methods of non-isothermal analysis. Results suggested that atomic rearrangement during glass transition is more complex than crystallization, and growth poses greater challenges than nucleation. Isothermal analysis conducted in the supercooled liquid region provides evidence of crystallization being controlled by diffusion, with a calculated mean Avrami exponent of 2.2. Additionally, the findings of fragility studies and kinetic studies demonstrated a strong correlation with the glass-forming ability (GFA), thereby validating the high GFA of the BMG analyzed in this study. Thus, this research results provide a detailed understanding of the complex crystallization kinetics, thermal behavior, and GFA of (Cu50Zr43Al7)98Y2 BMG, emphasizing its potential in materials science applications.

Effective optimization of atomic decoration in giant and superstructurally ordered crystals with machine learning.

Crystals with complicated geometry are often observed with mixed chemical occupancy among Wyckoff sites, presenting a unique challenge for accurate atomic modeling. Similar systems possessing exact occupancy on all the sites can exhibit superstructural ordering, dramatically inflating the unit cell size. In this work, a crystal graph convolutional neural network (CGCNN) is used to predict optimal atomic decorations on fixed crystalline geometries. This is achieved with a site permutation search (SPS) optimization algorithm based on Monte Carlo moves combined with simulated annealing and basin-hopping techniques. Our approach relies on the evidence that, for a given chemical composition, a CGCNN estimates the correct energetic ordering of different atomic decorations, as predicted by electronic structure calculations. This provides a suitable energy landscape that can be optimized according to site occupation, allowing the prediction of chemical decoration in crystals exhibiting mixed or disordered occupancy, or superstructural ordering. Verification of the procedure is carried out on several known compounds, including the superstructurally ordered clathrate compound Rb8Ga27Sb16 and vacancy-ordered perovskite Cs2SnI6, neither of which was previously seen during the neural network training. In addition, the critical temperature of an order-disorder phase transition in solid solution CuZn is probed with our SPS routines by sampling site configuration trajectories in the canonical ensemble. This strategy provides an accurate method for determining favorable decoration in complex crystals and analyzing site occupation at unprecedented speed and scale.

Exfoliatable Layered 2D Honeycomb Crystals of Host-guest Complexes Networked by CH-π Hydrogen Bonds.

Studies of graphene show that robust chemical bonds such as covalent bonds with trigonal-planar atoms afford layered atomic 2D crystals possessing unique properties. Although layered molecular crystals are of interest to diversify elements and structures of 2D materials, the structural diversity of molecules as well as weak intermolecular interactions inevitably makes the design to be one-off and individual. We herein report a versatile method to assemble layered molecular crystals. By developing a D3-symmetry host at vertices to form a honeycomb layer, a diverse range of layered 2D host-guest crystals were obtained. Substituents on the host, elements/structures of the guest, the stereochemistry of the host and types of intercalants were diversified, which should allow for 6×32×3×2 combinations for structural diversification.

Real space method for HAADF image simulation

A new real space HAADF simulation method was described in detail and a Real Space- STEM software was developed based on the new simulation method. The algorithm of the real space method can quickly calculate and simulate the microstructure images of complex crystals. The Real Space-STEM software developed in this paper has the functions of HRTEM and HAADF image simulation based on the real space method. By using this software to simulate high-resolution images of representative crystal materials from each crystal system, the HAADF images are both accurate and efficient. The effect of STEM parameters on HAADF imaging has been discussed using simulation results.

Podophyllotoxin derivatives-tubulin complex reveals a potential binding site of tubulin polymerization inhibitors in α-tubulin adjacent to colchicine site

The colchicine site of β-tubulin has been proven to be essential binding sites of microtubule polymerization inhibitors. Recent studies implied that GTP pocket of α-tubulin adjacent to colchicine sites is a potential binding site for developing tubulin polymerization inhibitors. However, the structural basis for which type of structural fragments was more beneficial for enhancing the affinity of α-tubulin is still unclear. Here, podophyllotoxin derivatives-tubulin complex crystals indicated that heterocyclic with the highly electronegative and small steric hindrance was conducive to change configuration and enhance the affinity of the residues in GTP pocket of α-tubulin. Triazole with lone-pairs electrons and small steric hindrance exhibited the strongest affinity for enhancing affinity of podophyllotoxin derivatives by forming two hydrogen bonds with αT5 Ser178. Pyrimidine with the secondary strong affinity could bind Asn101 to make the αH7 configuration deflection, which reduces the stability of tubulin result in its depolymerization. Conversely, 4β-quinoline-podophyllotoxin with the weakest affinity did not interact with α-tubulin. The molecular dynamics simulation and protein thermal shift results showed that 4β-triazole-podophyllotoxin-tubulin was the most stable mainly due to two hydrogen bonds and the higher van der Waals force. This work provided a structural basis of the potential binding sites for extending the α/β-tubulin dual-binding sites inhibitors design strategy.

Evaluation of Ammonium Nitrate(V) Morphology and Porosity Obtained by SEM and Tomography Imaging.

This paper presents an evaluation of the morphology of fertilizer-grade and prill-grade ammonium nitrate(V). All samples were analyzed using X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and tomography techniques. The XRD results revealed that despite various provenances, all samples exhibited similar Pmmm symmetry and diffraction patterns. SEM images indicated that prill ammonium nitrate(V) showed a more complex external and internal crystal structure than fertilizer-grade counterparts. Furthermore, tomography analysis revealed that each prill ammonium nitrate(V) sample demonstrated distinct porosity characteristics, including varying pore sizes and distribution patterns. Both methods confirmed that fertilizer-grade ammonium nitrate(V) in the cross-section had a pumice structure, and porous prill ammonium nitrate(V) had a rather complex structure, with a central cavity observed only in the case of Sample 4. The appearance of a central cavity can be explained by the different conditions or manufacturing processes of porous prill ammonium nitrate(V). Moreover, the fertilizer-type ammonium nitrate(V) exhibited the lowest surface-to-volume ratio of ca. 21% compared to the porous-type ammonium nitrate(V). This, together with the lowest surface area of ca. 116 mm2, confirmed the lowest absorption capacity of the fertilizer-grade ammonium nitrate(V) disclosed by the ammonium nitrate(V) producer.

Reproducible high-quality perovskite single crystals by flux-regulated crystallization with a feedback loop

Controlling the linear growth rate, a critical factor that determines crystal quality, has been a challenge in solution-grown single crystals due to complex crystallization kinetics influenced by multiple parameters. Here we introduce a flux-regulated crystallization (FRC) method to directly monitor and feedback-control the linear growth rate, circumventing the need to control individual growth conditions. When applied to metal halide perovskites, the FRC maintains a stable linear growth rate for over 40 h in synthesizing CH3NH3PbBr3 and CsPbBr3 single crystals, achieving outstanding crystallinity (quantified by a full width at half-maximum of 15.3 arcsec in the X-ray rocking curve) in a centimetre-scale single crystal. The FRC is a reliable platform for synthesizing high-quality crystals essential for commercialization and systematically exploring crystallization conditions, maintaining a key parameter—the linear growth rate—constant, which enables a comprehensive understanding of the impact of other influencing factors.

Enhanced Catalytic Activity of Crystalline Phosphorus Nanosheets Fabricated via Solvothermal Phase Transformation.

The newly reported crystalline phosphorus nanosheets (cryst-P NSs) exhibit promising features for industrial applications, including outstanding air-water stability and facile large-scale production. However, their complex crystallization impedes a priori tailoring. Herein, the temporal evolution of cryst-P NSs was investigated with the optimized synthesis parameters. The occurrence of self-assembly and solid-state rearrangement unveiled the existence of an intermediate phase as the bulk crystalline precursor and the predominance of nonclassical crystallization pathway(s). With the upgraded synthesis protocol simultaneously strengthening the merits of cryst-P NSs, their catalytic performances were evaluated in various electro- and/or photocatalytic reactions spanning hydrogen and oxygen evolution, full water splitting, CO2 reduction, and organic pollutant decomposition. Superior catalytic activities and orders of magnitude longer lifetimes were consistently discerned compared with the widely employed black phosphorus nanosheets with similar size and thickness. The exciting discoveries in both fundamental crystallization and catalytic applications drastically thrust the comprehension of elemental phosphorus, shedding light on the encouraging capabilities of solvothermal synthesis strategies in the design and systematic tailoring of phosphorus materials.

New cadmium(II) coordination complexes based on pentaatomic N-heterocycles and thiocyanate ion as ligands: Synthesis, crystal structure, spectroscopic characterizations, and Hirshfeld surface analysis

Two novel cadmium(II) coordination complexes, [Cd(bpt)2(SCN)2] 1 and [Cd2(bpo)(µ-SCN)4]n2, (bpt = 2,5-bis(pyridin-2-yl)-1,3,4-thiadiazole and bpo = 2,5-bis(pyridin-2-yl)-1,3,4-oxadiazole), have been synthesized and fully characterized by using FTIR, NMR, and UV–Vis spectroscopic techniques, as well as single crystal X-ray diffraction (SC-XRD). The complex 1 is a mononuclear, while the complex 2 is coordination polymer where bpo ligand and SCN−are in bridging modes, with two non-equivalent Cd ions. The coordination geometry is distorted octahedral in both complexes. The crystal of complex 1 is stabilized by C–H⋯N/C/S hydrogen bonds and π⋯π stacking interactions while the crystal packing of polymeric complex 2 is stabilized by C–H⋯S and π⋯π stacking interactions. Hirshfeld surface analysis was undertaken to investigate further the intermolecular interactions responsible for stabilization of the supramolecular assembly of 1 and 2. The calculated band gap energy (Eg) values of the Cd(II) complexes from the UV–Vis spectra indicated interesting semiconducting properties.

Structure and Stability of Ago2 MID-Nucleotide Complexes: All-in-One (Drop) His6-SUMO Tag Removal, Nucleotide Binding, and Crystal Growth.

The middle (MID) domain of eukaryotic Argonaute (Ago) proteins and archaeal and bacterial homologues mediates the interaction with the 5'-terminal nucleotide of miRNA and siRNA guide strands. The MID domain of human Ago2 (hAgo2) is comprised of 139 amino acids with a molecular weight of 15.56 kDa. MID adopts a Rossman-like beta1-alpha1-beta2-alpha2-beta3-alpha3-beta4-alpha4 fold with a nucleotide specificity loop between beta3 and alpha3. Multiple crystal structures of nucleotides bound to hAgo2 MID have been reported, whereby complexes were obtained by soaking ligands into crystals of MID domain alone. This protocol describes a simplified one-step approach to grow well-diffracting crystals of hAgo2 MID-nucleotide complexes by mixing purified His6-SUMO-MID fusion protein, Ulp1 protease, and excess nucleotide in the presence of buffer and precipitant. The crystal structures of MID complexes with UMP, UTP and 2'-3' linked α-L-threofuranosyl thymidine-3'-triphosphate (tTTP) are presented. This article also describes fluorescence-based assays to measure dissociation constants (Kd) of MID-nucleotide interactions for nucleoside 5'-monophosphates and nucleoside 3',5'-bisphosphates. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Crystallization of Ago2 MID-nucleotide complexes Basic Protocol 2: Measurement of dissociation constant Kd between Ago2 MID and nucleotides.

Insights into the crystallisation pathways in as-cast Ti40Zr10Cu36Pd14 glassy alloys

Biocompatible titanium-based bulk metallic glasses (Ti-based BMGs) are attractive for application in minimally invasive medical devices. They present a desirable set of properties, including low Young's modulus (E ≈ 100 GPa) and high yield strength (σ ≈ 2000 MPa). However, their implementation into practical applications is in part hindered by their limited glass forming ability (GFA) compared to BMG systems already commercialised. Due to their limited GFA, Ti-BMGs are more susceptible to crystallisation. This study investigates the crystalline heterogeneities found in Ti40Zr10Cu36Pd14 (at.%) glasses cast in automated equipment operating under close-to-industrial conditions. Distinct categories of crystallites are identified through microstructural observations and statistical analyses. Insight is provided on the complex crystallisation pathways that may be followed during cooling. Beyond the scientific contribution, the results indicate directions for the development and improvement of the manufacturing of Ti40Zr10Cu36Pd14.

Mapping Hydrogen Positions along the Proton Transfer Pathway in an Organic Crystal by Computational X-ray Spectra.

Understanding proton transfer (PT) dynamics in condensed phases is crucial in chemistry. We computed a 2D map of N 1s X-ray photoelectron/absorption spectroscopy (XPS/XAS) for an organic donor-acceptor salt crystal against two varying N-H distances to track proton motions. Our results provide a continuous spectroscopic mapping of O-H···N↔O-··· H+-N processes via hydrogen bonds at both nitrogens, demonstrating the sensitivity of N 1s transient XPS/XAS to hydrogen positions and PT. By reducing the O-H length at N1 by only 0.2 Å, we achieved excellent theory-experiment agreement in both XPS and XAS. Our study highlights the challenge in refining proton positions in experimental crystal structures by periodic geometry optimizations and proposes an alternative scaled snapshot protocol as a more effective approach. This work provides valuable insights into X-ray spectra for correlated PT dynamics in complex crystals, benefiting future experimental studies.