Search Results (69)

The determination of tungsten oxidation states and W–ligand bond lengths for pyranopterin tungsten enzymes can be negatively impacted by Fourier series termination effects and photodamage/photoreduction in the X-ray beam. As a result, a new set of bond valence sum (BVS) parameters have been derived from bond length data on W(+4) and W(+6) model compounds that were obtained from X-ray crystallography. These new W enzyme-specific BVS parameters have been used in the analysis of pyranopterin tungsten enzyme structural data. The results of this analysis indicate that there are potential issues with the enzyme crystal structures, including the number of ligating atoms to the tungsten atom, the W–ligand bond lengths, and the W oxidation state. We conclude that a BVS analysis of crystallographic and EXAFS structural data will help address these issues, and EXAFS should be more routinely employed in the determination of pyranopterin tungsten enzyme active site structures due to the increased accuracy of this technique for the determination of W–ligand bond distances. Full article

A study of the solid-state intermolecular interactions of twenty-nine benzopyrans substituted with polyhaloalkyl groups was carried out by quantum chemical calculations using the Mercury and WinGX computer programs. Molecular structures were obtained from crystallographic information files (CIF) of the CCDC database. C-H—O, C-H—X, C-X—O and C-X—X type contacts, characterized as unconventional hydrogen bonds, were identified and calculated. The criteria used for distances and angles were d(D—A) < R(D) + R(A) + 0.50 and d(H—A) < R(H) + R(A)—0.12°, where D-H—A > 100.0°. D is the donor atom, A is the acceptor atom, R is the Van der Waals radius and d is the interatomic distance. In addition, Etter’s notation was used to describe sets of hydrogen bonds in organic crystals, detailing the intermolecular contacts and periodic arrangements of the crystal packing. It was corroborated that certain positions of halogen atoms and their interactions play an important role in stabilizing the crystal lattice. Full article

Identifying the grain distribution and grain boundaries of nanoparticles is important for predicting their properties. Experimental methods for identifying the crystallographic distribution, such as precession electron diffraction, are limited by their probe size. In this study, we developed an unsupervised learning method by applying a Gabor filter to HAADF-STEM images at the atomic level for image segmentation and automatic counting of grains in polycrystalline nanoparticles. The methodology comprises a Gabor filter for feature extraction, non-negative matrix factorization for dimension reduction, and K-means clustering. We set the threshold distance and angle between the clusters required for the number of clusters to converge so as to automatically determine the optimal number of grains. This approach can shed new light on the nature of polycrystalline nanoparticles and their structure–property relationships. Full article

Although the crystals of coordination polymer {[CuCl(μ-O,O’-L-Br₂Tyr)]}n (1) (L-Br₂Tyr = 3,5-dibromo-L-tyrosine) were formed under basic conditions, crystallographic studies revealed that the OH group of the ligand remained protonated. Two adjacent [CuCl(L-Br₂Tyr)] monomers, bridged by the carboxylate group of the ligand in the syn-anti bidentate bridging mode, are differently oriented to form a polymeric chain; this specific bridging was detected also by FT-IR and EPR spectroscopy. Each Cu(II) ion in polymeric compound 1 is coordinated in the xy plane by the amino nitrogen and carboxyl oxygen of the parent ligand and the oxygen of the carboxyl group from the symmetry related ligand of the adjacent [Cu(L-Br₂Tyr)Cl] monomer, as well as an independent chlorine ion. In addition, the Cu(II) ion in the polymer chain participates in long-distance intermolecular contacts with the oxygen and bromine atoms of the ligands located in the adjacent chains; these intramolecular contacts were also supported by NCI and NBO quantum chemical calculations and Hirshfeld surface analysis. The resulting elongated octahedral geometry based on the [CuCl(L-Br₂Tyr)] monomer has a lower than axial symmetry, which is also reflected in the symmetry of the calculated molecular EPR g tensor. Consequently, the components of the d-d band obtained by analysis of the NIR-VIS-UV spectrum were assigned to the corresponding electronic transitions. Full article

Select triphenyl stannanes bearing either a formally sp² or sp³ hybridized amine, viz 2-(pyC₂H₄)SnPh₃ (2: py = pyridinyl), 4-(pyC₂H₄)SnPh₃ (3), 2-(pzC₂H₄)SnPh₃ (4: pz = pyrazyl), and Me₂N(CH₂)₃SnPh₃ (6), were prepared and characterized by NMR spectroscopy (¹¹⁹Sn, ¹³C, ¹H), and additionally, in the case of 2, by single crystal X-ray diffraction. Bromination of 2 to yield 2-(pyC₂H₄)SnPhBr₂ (8) was achieved in good yield. X-ray crystallographic analysis of 8 revealed two unique molecules with 5-coordinate Sn centers featuring Sn-N distances of 2.382 (5) and 2.363 (5) Å, respectively. The calculated structures of the non- and hypercoordinating C,N-stannanes (1–9) were in good agreement with available crystallographic data. The relative stabilities of hyper- and non-hypercoordinating conformers obtained from conformational sampling were determined by comparison with reference conformers and by natural bond orbital (NBO) energetic analyses. Reduction of 8 to the dihydride species, 2-(pyC₂H₄)SnPhH₂ (9), and subsequent conversion to the polystannane, -[2-(pyC₂H₄)SnPh]_n- (15), by transition metal-catalyzed dehydropolymerization was also achieved. Evidence for the decomposition of 15 into a redistributed distannoxane, {2-(pyC₂H₄)SnPh₂}₂O (16), was also observed. Full article

Vanadium complexes have gained considerable attention as biologically active compounds. In this contribution, three previously reported dioxovanadium(V) complexes with pyridoxal semicarbazone, thiosemicarbazone, and S-methyl-iso-thiosemicarbazone ligands are theoretically examined. The intermolecular stabilization interactions within crystallographic structures were investigated by Hirshfeld surface analysis. These experimental structures were optimized at the B3LYP-D3BJ/6-311++G(d,p)(H,C,N,O,S)/def2-TZVP(V) level of theory, and crystallographic and optimized bond lengths and angles were compared. High correlation coefficients and low mean absolute errors between these two data sets proved that the selected level of theory was appropriate for the description of the system. The changes in structures and stability were examined by adding explicit solvent molecules. The Quantum Theory of Atoms in Molecules (QTAIM) was employed to analyze the intramolecular interactions with special emphasis on the effect of substituents. A good correlation between electron density/Laplacian and interatomic distance was found. Through molecular docking simulations towards Bovine Serum Albumin (BSA), the binding affinity of complexes was further investigated. The spontaneity of binding in the active position of BSA was shown. Further experimental studies on this class of compounds are advised. Full article

ENA transporters are a group of P-type ATPases that are characterized by actively moving Na⁺ or K⁺ out of the cell against their concentration gradient. The existence of these transporters was initially attributed to some fungi, although more recently they have also been identified in mosses, liverworts, and some protozoa. Given the current increase in the number of organisms whose genomes are completely sequenced, we set out to expand our knowledge about the existence of ENA in organisms belonging to other phylogenetic groups. For that, a hidden Markov model profile was constructed to identify homologous sequences to ENA proteins in protein databases. This analysis allowed us to identify the existence of ENA-type ATPases in the most primitive groups of fungi, as well as in other eukaryotic organisms not described so far. In addition, this study has allowed the identification of a possible new group of P-ATPases, initially proposed as ENA but which maintain phylogenetic distances with these proteins. Finally, this work has also addressed this study of the structure of ENA proteins, which remained unknown due to the lack of crystallographic data. For this purpose, a 3D structure prediction of the NcENA1 protein of the fungus Neurospora crassa was performed using AlphaFold2 software v2.3.1. From this structure, the electrostatic potential of the protein was analyzed. With all these data, the protein regions and the amino acids involved in the transport of Na⁺ or K⁺ ions across the membrane were proposed for the first time. Targeted mutagenesis of some of these residues has confirmed their relevant participation in the transport function of ENA proteins. Full article

The reaction of Tb³⁺ ions with KAu(SCN)₂ results in the formation of the crystalline coordination compound Tb[Au(SCN)₂]₃·6H₂O. Single-crystal X-ray diffraction has been employed to investigate the structural features of this compound. The crystallographic data are as follows (Mo K_α, λ = 0.71073 Å): orthorhombic, Cmcm, a = 12.4907(9) Å, b = 8.5845(6) Å, c = 20.7498(8) Å, V = 3679.72(16) ų, Z = 4, R₁(I > 2(σ)) = 0.0232. This material represents the first known example of a lanthanide dithiocyanatoaurate compound. Au(SCN)₂⁻ anions bridge Tb³⁺ centers in a bidentate fashion to form the [Tb(H₂O)₄(Au(SCN)₂)₂]͚⁺ 1D chains present in the structure. Trimeric Au units in the structure contain short aurophilic bonding interactions with distances of 3.1066(4) Å. The more common O–H‧‧‧O and O–H‧‧‧N H-bonding interactions in the structure are overshadowed by relatively rare O–H‧‧‧S interactions involving the bis(thiocyanato)gold(I) anions. Photoluminescence measurements illustrate that Tb[Au(SCN)₂]₃·6H₂O displays strong Tb³⁺-based emission, but there is a lack of Au-based emission down to 85 K. Excitation spectra are recorded for the title compound and these measurements demonstrate the presence of a donor–acceptor process within the compound, leading to enhanced Tb³⁺-based emission. Full article

The effect of graphene (GR) on Ni surface relaxation and reconstruction in three different substrate orientations, {111}, {001}, and {011}, at two different temperatures, 300 K and 400 K, was studied using molecular dynamics simulation. The change in the interplanar distances of the substrate and redistribution of Ni and C atoms in a direction perpendicular to the surface was compared with the equilibrium state of GR and bulk Ni, in the absence of the counterpart. The surface reconstruction for the GR/Ni system was analyzed based on the calculated radial pair distribution functions of Ni and C atoms. The surface roughness was visualized using 2D atomic distribution maps. The introduction of GR on the Ni surface in any crystallographic orientation decreases the maximum modification of interplanar spacing compared to the bulk by less than 1%. For the studied substrate orientations and temperatures, it was found that the most densely packed {111} orientation of the Ni base provides minimal changes in the structural parameters of both counterparts at 400 K. Additionally, the system formed by GR deposition on Ni {111} at 400 K is characterized by the least roughness. Full article

Blatter radicals 1-(3,4-difluorophenyl)-(1a) and 1-(2,4-difluorophenyl)-3-phenyl-1,4-dihydrobenzo[e][1,2,4]triazin-4-yl (1b) were prepared in good yields through oxidation of the corresponding amidrazones using MnO₂ in dry CH₂Cl₂. Cyclic voltammetry showed that both radicals are oxidized and reduced chemically and electrochemically reversibly in accordance with −1/0 and 0/+1 processes. EPR spectroscopy indicated that spin density is mainly delocalized on the triazinyl moiety of the heterocycle. The structure of all paramagnets was unambiguously confirmed by single-crystal X-ray diffraction, and two different 1D chains of alternating radicals were identified. 3,4-difluorophenyl-derivatives 1a are packed into columns composed of two kinds of alternating centrosymmetric dimers, having comparatively short intermolecular distances. In crystals of 2,4-difluorophenyl-derivative 1b, the parallel arrangement of bicyclic moieties and phenyl rings favors the formation of 1D regular chains wherein the radicals are related by translation parallel to the crystallographic stacking axis. Magnetic susceptibility measurements in the 2–300 K region showed that in crystals of the radicals, strong antiferromagnetic interactions are dominant. Subsequent fitting of the dependence of χT on T with 12-membered looped stacks gave the following best-fit parameters: for 1a, g = 2.01 ± 0.05, J₁/k_B = −292 ± 10 K (according to BS-DFT calculations J₂ = 0.12 × J₁ and J₃ = 0.61 × J₁); for 1b, g = 2.04 ± 0.01 J₁/k_B = −222 ± 17 K. For comparison, in a nonfluorinated related radical, there are only very weak intermolecular interactions along the columns (J/k_B = −2.2 ± 0.2 K). These results illustrate the magnitude of the influence of the difluorophenyl substituents introduced into Blatter radicals on their structure and magnetic properties. Full article

Complexes of the alkali metals Li-Cs with 3-thiophenecarboxylate (3tpc), 2-methyl-3-furoate (2m3fur), 3-furoate (3fur), 4-hydroxycinnamate (4hocin), and 4-hydroxybenzoate (4hob) ions were prepared via neutralisation reactions, and the structures of [Li₂(3tpc)₂]_n (1Li); [K₂(3tpc)₂]_n (1K); [Rb(3tpc)(H₂O)]_n (1Rb); [Cs{H(3tpc)₂}]_n (1Cs); [Li₂(2m3fur)₂(H₂O)₃] (2Li); [K₂(2m3fur)₂(H₂O)]_n (2K); [Li(3fur)]_n(3Li); [K(4hocin](H₂O)₃]_n (4K); [Rb{H(4hocin)₂}]_n.nH₂O (4Rb); [Cs(4hocin)(H₂O)]_n (4Cs); [Li(4hob)]_n (5Li); [K(4hob)(H₂O)₃]_n (5K); [Rb(4hob)(H₂O)]_n (5Rb); and [Cs(4hob)(H₂O)]_n (5Cs) were determined via X-ray crystallography. Bulk products were also characterised via XPD, IR, and TGA measurements. No sodium derivatives could be obtained as crystallographically suitable single crystals. All were obtained as coordination polymers with a wide variety of carboxylate-binding modes, except for dinuclear 2Li. Under conditions that normally gave coordinated carboxylate ions, the ligation of hydrogen dicarboxylate ions was observed in 1Cs and 4Rb, with short H-bonds and short O…O distances associated with the acidic hydrogen. The alkali-metal carboxylates showed corrosion inhibitor properties inferior to those of the corresponding rare-earth carboxylates. Full article

Crystals of NaSn₂F₅ were obtained from an aqueous solution. Their morphology and habitus were studied via scanning electron microscopy and X-ray phase diffraction analysis. The crystals obtained have a long prismatic shape with a very large aspect ratio (>100). The faceting of the crystal is represented by the (110) face, while the (100) face is practically absent. A nanocomposite incorporating one-dimensional (1D) NaSn₂F₅@SWCNT crystals was synthesized from the melt by means of the capillary wetting technique. The embedded fragment is represented by two planes of Sn cations, which provide contrast in high-resolution electron microscopy images. The cation plane is represented by the (110) crystallographic plane of the NaSn₂F₅ structure. The crystallographic direction [2$\overline{2}$3] coincides with the nanotube axis. The first layer of Sn cations forms a hexagonal network with Sn atoms at its nodes. The tin atoms in the second layer are arranged according to the closest spherical packing law in a plane, but with a distance between atoms that is two times greater than that in the first layer. Sn cations’ hexagon sizes are ~0.87 nm and ~0.69 nm in size. According to the Raman spectroscopy data, the nanocomposite behaves as an electron acceptor. The SWCNT diameter of 1.54 nm revealed using NaSn₂F₅@SWCNT Raman spectroscopy corresponds to their diameter in electron microscope images and the diameter used for modeling. Full article

G protein-coupled receptors (GPCRs) are the largest class of drug targets and undergo substantial conformational changes in response to ligand binding. Despite recent progress in GPCR structure determination, static snapshots fail to reflect the conformational space of putative binding pocket geometries to which small molecule ligands can bind. In comparative modeling of GPCRs in the absence of a ligand, often a shrinking of the orthosteric binding pocket is observed. However, the exact prediction of the flexible orthosteric binding site is crucial for adequate structure-based drug discovery. In order to improve ligand docking and guide virtual screening experiments in computer-aided drug discovery, we developed RosettaGPCRPocketSize. The algorithm creates a conformational ensemble of biophysically realistic conformations of the GPCR binding pocket between the TM bundle, which is consistent with a knowledge base of expected pocket geometries. Specifically, tetrahedral volume restraints are defined based on information about critical residues in the orthosteric binding site and their experimentally observed range of C_α-C_α-distances. The output of RosettaGPCRPocketSize is an ensemble of binding pocket geometries that are filtered by energy to ensure biophysically probable arrangements, which can be used for docking simulations. In a benchmark set, pocket shrinkage observed in the default RosettaGPCR was reduced by up to 80% and the binding pocket volume range and geometric diversity were increased. Compared to models from four different GPCR homology model databases (RosettaGPCR, GPCR-Tasser, GPCR-SSFE, and GPCRdb), the here-created models showed more accurate volumes of the orthosteric pocket when evaluated with respect to the crystallographic reference structure. Furthermore, RosettaGPCRPocketSize was able to generate an improved realistic pocket distribution. However, while being superior to other homology models, the accuracy of generated model pockets was comparable to AlphaFold2 models. Furthermore, in a docking benchmark using small-molecule ligands with a higher molecular weight between 400 and 700 Da, a higher success rate in creating native-like binding poses was observed. In summary, RosettaGPCRPocketSize can generate GPCR models with realistic orthosteric pocket volumes, which are useful for structure-based drug discovery applications. Full article

For industrial processes in which refractory metals are necessary, hafnium carbonitride exhibits excellent performance due to its high thermal conductivity and resistance to oxidation. In this study, hafnium carbonitride was deposited on Inconel 718 steel and silicon (100) substrates. The objective was to characterize the wear properties as a function of temperature. The layers were deposited by physical vapor deposition (PVD) in an R.F. sputtering magnetron system from carbon targets and high-purity hafnium (99.99%). The wear tests were carried out at temperatures of 100 °C, 200 °C, 400 °C, and 800 °C in non-lubricated conditions. The coefficient of friction (COF) was recorded in situ. The heat treatment temperature on coatings is essential in determining anti-wear efficiency. It was determined that high temperatures (800 °C) improve resistance to wear. High-resolution XPS spectra were used to detect the chemical states of Hf 4f_5/2 and Hf 4f_7/2. The 4f_5/2 and 4f_7/2 binding energy indicates the presence of HfN and HfC. Using the TEM technique in bright field mode allowed us to know the orientation, crystallographic structure and interplanar distances of the HfCN. The topography of the coatings, by AFM, shows uniform grains and very small characteristics that determine the low surface roughness value. The SEM image of the cross-section of the HfCN coating shows homogeneity of the layer; no cracks or deformations are observed. Full article

This paper presents the results of research on a newly developed surface layer made by laser remelting the working surface of the Cu-ETP (CW004A, Electrolytic Tough Pitch) copper section insulator guide with Cr-Al powder. For the investigation, a fibre laser was used with relatively high power, reaching 4 kW, so as to ensure a high gradient of cooling rate for microstructure refinement. The microstructure of the transverse fracture of the layer (SEM) and the distribution of elements in the microareas (EDS) were investigated. The test results showed that chromium does not dissolve in the Cu matrix, and its precipitates take the shape of dendrites. The hardness and thickness of the surface layers as well as the friction coefficient and the influence of the Cr-Al powder feeding speed on them were examined. For the distance from the surface to 0.45 mm, the hardness of the produced coatings is above 100 HV_0.3, while the friction coefficient of the produced coatings is in the range of 0.6–0.95. More sophisticated investigation results concern the d-spacing lattice parameters of the crystallographic structure of the obtained Cu phase reaching the range between 3.613–3.624 Å. Full article