Crystallography Reports最新文献

A vaccine prototype against dengue virus was designed based on the analysis of the outer-membrane domains of the dengue virus capsid protein. In order to predict the epitope structures, the three-dimensional structures of the domains were modeled using the AlphaFold2 artificial intelligence system. The retention of the structural stability of all studied subdomains was demonstrated by molecular dynamics simulations of vaccine candidates using the Gromacs-2023 program package. The ability of the vaccine candidate to induce a pronounced primary cell immune response and a stable secondary immune response was predicted with the C-IMMSIMM server.

A methodology for measuring and taking into account the background in a single-crystal neutron experiment with a position-sensitive detector is proposed. This methodology makes it possible to increase the ratio of integrated intensities to the standard deviation I/σ(I) for diffraction reflections and thereby supplement the experimental dataset with weak reflections that previously did not meet the condition I/σ(I) > 3 and were not taken into account in crystallographic calculations. The methodology was tested on experimental data during structural studies of Cs₄(HSO₄)₃(H₂PO₄) crystals on the MOND diffractometer at the IR-8 reactor of the National Research Centre “Kurchatov Institute.”

The results of microscopic and X-ray studies of polymorphic transformations II ↔ I in K_0.945Rb_0.055NO₃ are discussed. It is shown that the transformations II ↔ I in the studied crystal are enantiotropic in nature and occur with the formation and growth of nuclei of the daughter modification inside the matrix. The equilibrium temperature between the II and I modifications is Т₀ = 455 ± 0.5 K. It is determined that in K_0.945Rb_0.055NO₃ the transformation II ↔ I is of a single crystal–single crystal nature.

The transformation of the PdBi compound at high temperatures has been studied using in situ high-temperature single-crystal X-ray diffraction. New data on the crystal structure of the high-temperature PdBi modification have been obtained. The PdBi structure at T = 293, 373, 423, and 473 K is orthorhombic (sp. gr. Cmc2₁) with the lattice parameters a = 8.7160(3) Å, b = 7.2031(3) Å, c = 10.6631(4) Å, V = 669.45(4) ų, and Z = 16 (293 K). Upon further heating, a phase transition to the high-temperature modification occurs. The PdBi structure at T = 523 and 573 K has been solved in the orthorhombic sp. gr. Cmcm, a = 3.6162(3) Å, b = 10.6446(8) Å, c = 4.4208(4) Å, V = 170.17(3) ų, and Z = 4 (523 K).

Complex structural studies of nanosized bismuth-doped yttrium iron garnet (BYIG) films have been performed using X-ray diagnostics, scanning/transmission electron microscopy, and energy-dispersive X-ray microanalysis. The crystal structure of the film–substrate interface and near-surface layers, along with the change in the interplanar distance over the film thickness, have been determined. The following features of the film microstructure were revealed: the presence of pores, the absence of misfit dislocation at the interface, the formation of maghemite (γ-Fe₂O₃) particles on the film surface, and a decrease in the Bi content towards the film surface. Suggestions about the influence of the Bi content on the magneto-optical properties in dependence of the film thickness are made.

The review presents the results of the extensive study of the new anhydrous minerals discovered in the fumaroles of the Tolbachik volcano (Kamchatka) during the last 10 years. The conditions for the synthesis of fumarolic mineral analogues and the features of their crystal chemistry are described. The emphasis is given to the minerals containing sulfate or vanadate anions, the discovery of which gave rise to large families of inorganic compounds and materials with rich and interesting crystal chemistry. A separate section is devoted to the progress in the field of high-temperature X-ray diffraction study of exhalative minerals. Several rare topotactic single crystal to single crystal (SC–SC) transformations detected for vergasovaite and aleutite are described.

The major milestones in the centennial history of the Department of Crystallography of St. Petersburg State University, the oldest of the existing departments of crystallography in Russia, are considered. It is shown that the St. Petersburg scientific crystallographic school originates from the great Russian scientist E.S. Fedorov (1853–1919). The main areas of the scientific activity of the staff (crystal morphology, crystal optics, crystal growth, crystal chemistry, crystal physics, X-ray diffraction analysis) are described, and biographical information about the heads of the department (O.M. Ansheles, V.B. Tatarsky, V.A. Frank-Kamenetsky, S.K. Filatov, Y.O. Punin) is given.

Data on the thermal properties of about 200 oxygen compounds, built from triangular (borates, carbonates, nitrates) and tetrahedral (silicates, sulfates) groups are summarized. An analysis of the dependence of the volumetric thermal expansion coefficient α_V  of these compounds and their melting points is carried out in accordance with the systematics by S.K. Filatov, based on the value of the residual charge Z per one anionic polyhedron beyond this polyhedron. The residual charge Z of an anionic group characterizes the degree of polymerization of such groups. This approach is used for mixed groups (tetrahedral with different charges of the central atom) and developed for heteropolyhedral anionic groups (both oxygen triangles and tetrahedra in borates). It has been shown that the volumetric thermal expansion increases and the melting temperature decreases with a decrease in the residual charge Z due to the rise in the degree of condensation of anionic groups and weakening in the strength of the cation–oxygen bonds. At the same residual charge Z of the anionic group, the spread of α_V values makes it possible to reveal the influence of the cation charge and size: thermal expansion increases as the charge decreases and the cation radius increases. Among the studied oxygen compounds the structures with tetrahedra have minimal volumetric expansion (borates: 〈α_V〉₃ = 22 × 10⁻⁶, borosilicates: 〈α_V〉₂₇ = 29 × 10⁻⁶, aluminosilicates: 〈α_V〉₂₇ = 28 × 10⁻⁶, and silicates: 〈α_V〉₃₄ = 27 × 10⁻⁶ °С⁻¹). Compounds with triangular groups (borates: 〈α_V〉₃₂ = 41 × 10⁻⁶, carbonates: 〈α_V〉₁₀ = 40 × 10⁻⁶ °С⁻¹) and borates with mixed anion groups (〈α_V〉₄₀ = 43 × 10⁻⁶ °С⁻¹) exhibit intermediate values. Sulphates with isolated tetrahedra (〈α_V〉₂₁ = 90 × 10⁻⁶ °С⁻¹) and nitrates with isolated triangles (〈α_V〉₅ = 132 × 10⁻⁶ °С⁻¹) demonstrate maximal volumetric expansion values, which is caused by the weakening in the bonds beyond the anionic complex.

The geometrical aspects of packing of molecular crystals of cubic and hexagonal syngonies have been considered. It has been shown that, when asymmetric molecules are packed into a crystal, a fraction of the unit-cell regions forbidden for arrangement of molecules (forbidden volume) is one the main geometrical factors affecting the abundance of a particular group of symmetry. Symmetric molecules predominantly occupy particular orbitals, which correspond to the close and closest packings of spheres. A list of regular systems of space groups of symmetry of cubic and hexagonal singonies has been obtained, the regular systems of points of which can describe close packings of molecules in terms of the closest packings of spheres.

The data on the structures of the hydrotalcite-group minerals—layered double hydroxides with the general formula (M_{6}^{{2 + }}M_{2}^{{3 + }}{{({text{OH}})}_{{16}}}A_{{2/m}}^{{m-}})⋅4H₂O (М²⁺ = Mg²⁺, Ni²⁺; М³⁺ = Al³⁺, Fe³⁺, Cr³⁺, Mn³⁺, Co³⁺; A = ({text{CO}}_{3}^{{2 - }}), Cl^– and OH^–)—are summarized. It is shown that all of them crystallize with the structure of 3R- and 2H-polytypes without the formation of superstructures. Their unit-cell parameter a ranges within 3.05–3.13 Å. The characteristic interlayer distances d_00n for the group members with carbonate and chloride anions are ~7.80 and 8.04 Å, respectively (c = d_00n × 2 for 2H and c = d_00n × 3 for 3R). Three hydrotalcite-group minerals should be reconsidered taking into account the new crystallographic data and regularities: takovite and droninoite most likely correspond to minerals of the quintinite group with M²⁺ : M³⁺ = 2 : 1, rather than to the hydrotalcite-group minerals, and the data on reevesite indicate that this name could describe two minerals with M²⁺ : M³⁺ = 3 : 1 and 2 : 1.