Kristallografiâ

A peer-reviewed journal that publishes original articles, short communications, and reviews on various aspects of crystallography: diffraction and scattering of X-rays, electrons, and neutrons, determination of crystal structure of inorganic and organic substances, including proteins and other biological substances; UV–Vis and IR spectroscopy; growth, imperfect structure and physical properties of crystals; thin films, liquid crystals, nanomaterials, partially disordered systems, and the methods of studies.

The journal was founded in 1956.

Media registration certificate: № 0110215 от 08.02.1993

Founders: Russian Academy of Sciences, Shubnikov Institute of Crystallography of RAS

Editor-in-Chief: Michail V. Kovalchuk, corresponding member RAS, Doctor of Sc., Full Professor

Frequency / Access: 6 issues per year / Subscription

Included in: White list (2nd level), Higher Attestation Commission list, RISC

Current Issue

Open Access Open Access  Restricted Access Access granted  Restricted Access Subscription Access

Vol 69, No 6 (2024)

Cover Page

Full Issue

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

ДИФРАКЦИЯ И РАССЕЯНИЕ ИОНИЗИРУЮЩИХ ИЗЛУЧЕНИЙ

Experimental Study of the Method of X-ray Phase-Contrast Microscopy Using a Nanofocusing Lens at KISI-Kurchatov synchrotron source
Folomeshkin M.S., Kohn V.G., Seregin A.Y., Volkovsky Y.A., Prosekov P.A., Yunkin V.A., Snigirev A.A., Pisarevsky Y.V., Blagov A.E., Kovalchuk M.V.
Abstract

The results of an experimental study at the KISI-Kurchatov synchrotron source of a new phase-contrast imaging scheme for micro-objects using a nanofocusing compound refractive lens are presented. Visualization with submicron spatial resolution of a Fresnel zone plate, with the width of outer zones less than 0.5 µm, has been demonstrated. It was found that in the conducted experiments the main contribution to the instrumental function, which limits spatial resolution, is due to the vibrations of the optical scheme elements. The possibility of using the proposed scheme to determine the beam transverse size at the focus of the compound refractive lens, considering the instrumental function, is shown.

Kristallografiâ. 2024;69(6):919-926
pages 919-926 views

REAL STRUCTURE OF CRYSTALS

Peculiarities of formation of defects initiating fatigue faults in granular alloy EP741NP
Pavlov I.S., Artamonov M.A., Artemov V.V., Kumskov A.S., Marchukov E.Y., Vasiliev A.L.
Abstract

The samples of EP741NP alloy destroyed during fatigue testing were investigated by means of transmission electron microscopy, energy-dispersive X-ray microanalysis and electron diffraction. The composition and crystal structure of defects detected at the boundaries of fatigue cracks were studied in details. It was shown that such defects mainly have the morphology of elongated flat "carpets" containing NiO, CTixNb1–x, amorphous AlOx, HfO2, Al2O3, β-Al2O3, Al2MgO4, Co7Mo6, Co3O4, S4Ti3, NbO2, TiO2, as well as amorphous regions containing C, O, Ca, S, Na and Cl. Assumptions were made about the source and of time formation of the studied defects.

Kristallografiâ. 2024;69(6):927-937
pages 927-937 views

СТРУКТУРА НЕОРГАНИЧЕСКИХ СОЕДИНЕНИЙ

Defect crystal structure of α-Na0.5–xR0.5+xF2+2x (R = Dy–Lu, Y) on X-Ray and electron diffraction data. II. Defect structure of the α-Na0.4R0.6F2.2 (R = Ho–Lu, Y) nanostructured crystals
Sulyanova E.A., Sobolev B.P., Nikolaichik V.I., Avilov A.S.
Abstract

The α-Na0.4R0.6F2.2 crystals (R = Ho–Lu, Y) were studied by X-ray diffraction analysis at 293 and 85 K. A unified cluster model of nanostructured crystals with a fluorite-type structure based on the polymorphism of KR3F10 (R = Er, Yb) was used to model their defect structure. The α-Na0.4R0.6F2.2 matrix component contained Na+ and R3+ in a ratio of 1 : 1. Part of the matrix anions was shifted from 8c to 32f position (sp. gr. Fm3m). Excess R3+ cations formed with Na+ octa-cubic clusters with nuclei in the form of cuboctahedra {F12} formed by interstitial anions at the 48i position. The α-Na0.4R0.6F2.2 cluster component was formed by octa-cubic clusters of type i. The electron diffraction method showed that the clusters had the shape of plates about 5 nm thick with superstructural ordering. Their structural model based on the K0.265Gd0.735F2.47 structure was proposed. For the first time, experimental confirmation of the affiliation of α-Na0.5–xR0.5+xF2+2x to nanostructured crystals was obtained by electron diffraction. When the temperature decreases from 293 to 85 K, the type of cluster component of the defect α-Na0.4R0.6F2.2 structure with R = Ho–Lu, and Y was not change. At 293 K, the boundary of the type change of the defect structure in the α-Na0.5–xR0.5+xF2+2x series was located between R = Dy (with the Z = 66 atomic number) and Ho (with Z = 67). When the temperature drops from 293 to 85 K, the position of the boundary was not change.

Kristallografiâ. 2024;69(6):938-953
pages 938-953 views
Desymmetrization in eudialyte-group minerals. II. A role of м2-position in ordered р3-model of zr-rich member eudialyte group structure
Rastsvetaeva R.K., Aksenov S.M., Gridchina V.M., Chukanov N.V.
Abstract

A re-study of the crystal structure of low-calcium and high-zirconium eudialyte from the Khibiny Mountains of the Kola Peninsula has revealed new features of its structure, namely a decrease in the symmetry of the mineral. The ordering of the Ca, Fe, Mn and Na atoms within the octahedrons of six-membered rings, as well as the Zr and Na atoms in the M2 positions at the centre of the square pyramids, was established within the framework of P3 symmetry. The trigonal cell parameters are a = 14.222(3), c = 30.165(5) Å, and V = 5283.9 Å3. In light of the new data, the low-calcium eudialyte can be classified as either oneillite or raslakite, specifically a high-zirconium variety of the latter. The study of the structure of this mineral in rhombohedral symmetry (space group R3m and R3) and trigonal P3-symmetry has demonstrated that the reduction in structural symmetry of the low-calcium representatives of the eudialyte group allows for the clarification of the ordering of cations occupying pivotal positions within the framework.

Kristallografiâ. 2024;69(6):954-959
pages 954-959 views

STRUCTURE OF ORGANIC COMPOUNDS

Effect of different gaseous mediums in the process of microwave pyrolysis carbonization of cellulose on the properties of the obtained activated carbon
Dyachkova I.G., Zolotov D.A., Kumskov A.S., Volchkov I.S., Matveev E.V., Berestov V.V., Asadchikov V.E.
Abstract

A comparative study of the characteristics of high-molecular organic matter (cotton lint) subjected to pyrolytic carbonisation under conditions of high-intensity microwave radiation in various gaseous media (N2, CO2, Ar) has been conducted. The methods employed included the determination of adsorption activity through the use of a methylene blue indicator, X-ray fluorescence analysis, transmission electron microscopy with microanalysis, and X-ray phase analysis. Electrodes derived from carbon materials produced through microwave carbonisation with varying gases were constructed, and symmetric cells were assembled in accordance with the two-electrode configuration. The electrochemical properties were investigated using cyclic voltammetry and galvanostatic charge-discharge methods. The results demonstrated that the materials obtained using a CO₂ gaseous medium exhibited the most optimal characteristics.

Kristallografiâ. 2024;69(6):960-970
pages 960-970 views

STRUCTURE OF MACROMOLECULAR COMPOUNDS

Features of three-dimensional reconstruction of spirals based on small-angle x-ray scattering data
Grigorev V.A., Konarev P.V., Volkov V.V.
Abstract

The interest in spiral particles lies in their resemblance to authentic nanostructures that emerge through the self-organisation of biopolymers (such as carrageenans, DNA, and so forth). Conversely, the determination of the structural parameters of such particles based on small-angle scattering data is challenging due to the lack of conditioning in the inverse problem. This is demonstrated by the utilisation of established bead structure modelling software. This paper considers a modification of the search algorithm in a limited area of space and the behaviour of solutions depending on the values of the parameters of the objective function responsible for the connectivity and looseness of the structure, the type of weighing of the scattering intensity curve, and the width of the angular range of data. In order to statistically assess the stability of the solutions, a sequential model search mode was applied, with varying amounts of contributions of penalty terms. The empirical dependences of the optimal values of the search parameters with respect to the parameters of the distribution curve of paired distances were determined.

Kristallografiâ. 2024;69(6):971-980
pages 971-980 views
Protein of unknown function from variovorax paradoxus with amino acid substitution n174k is able to form schiff base with plp molecule
Ilyasov I.O., Minyaev M.E., Rakitina T.V., Bakunova A.K., Popov V.O., Bezsudnova E.Y., Boyko K.M.
Abstract

Pyridoxal-5'-phosphate (PLP)-dependent enzymes are one of the most widely represented groups of enzymes in organisms, performing more than 150 different catalytic functions. Based on the three-dimensional structure, members of this group are divided into seven (I-VII) different fold types. Cofactor binding in these enzymes occurs due to the formation of a Schiff base with a conserved lysine residue located in the active site. A recently discovered protein from the bacterium Variovorax paradoxus (VAPA), which belongs to the IV fold type and has significant structural similarity to transaminases, contains an asparagine residue at the catalytic lysine position in the transaminases and, as a result, cannot form a Schiff base with PLP and does not have aminotransferase activity. In this research, a point mutant of VAPA protein with the N174K substitution was obtained and its 3D structure was determined. Analysis of the structural data showed that the introduced mutation restores the ability of VAPAN174K to form a Schiff base with a cofactor.

Kristallografiâ. 2024;69(6):981-986
pages 981-986 views

КРИСТАЛЛОГРАФИЯ В БИОЛОГИИ И МЕДИЦИНЕ

Development of a subunit vaccine against virus of african svine virus based on cd2v protein with immunoinformatics and molecular dynamics methods
Ivanovsky A.S., Timofeev V.I., Kalach A.V., Kordonskaya Y.V., Marchenkova M.A., Pisarevsky Y.V., Dyakova Y.A., Kovalchuk M.V.
Abstract

A subunit vaccine against the African swine fever virus (ASF) has been designed using immunoinformatics and molecular dynamics methods. The three-dimensional structure of the selected immunogenic protein of the ASF-CD2v virus was modelled, and its topology relative to the membrane was predicted. B- and T-cell epitopes for the supramembrane part of CD2v were predicted, and their immunogenicity, allergenicity, and toxicity were evaluated. In order to facilitate the development of a subunit vaccine, the least variable site was identified on the basis of an analysis of the conservatism of the predicted epitopes. The stability of the selected supramembrane site in an aqueous salt solution was evaluated using molecular dynamics methods, and it was demonstrated that the site is structurally stable. The immunomodulation method has demonstrated that the developed candidate vaccine is capable of eliciting a sustained immune response and does not result in the development of a cytokine storm.

Kristallografiâ. 2024;69(6):987-997
pages 987-997 views

ДИНАМИКА РЕШЕТКИ И ФАЗОВЫЕ ПЕРЕХОДЫ

Linear and nonlinear dielectric response of vdf60/tr40 copolymer in the vicinity of ferroelectric phase transition
Verkhovskaya K.A., Pankova M.A., Popov I.I., Korotkov L.N.
Abstract

The effect of the bias electric field E= (0–10 kV/cm) on the dielectric properties of the VDF60/Tr40 copolymer was studied within the temperature range of 20–110°C. It was found that the dielectric nonlinearity De, is negative in the polar phase and becomes positive above the Curie temperature (TC). The increase in TC under the field E= is not uniform. At E= < Ec (Ec is the threshold field), the Curie temperature is practically independent of E=. At E= > Ec, the increase of TC is observed. The presence of the threshold field indicates the presence of sources of random electric fields in the material under study. It is assumed that they are responsible for the smearing of the ferroelectric phase transition.

Kristallografiâ. 2024;69(6):998-1003
pages 998-1003 views

ФИЗИЧЕСКИЕ СВОЙСТВА КРИСТАЛЛОВ

Spectral-luminescence and scintillation properties of p-terphenyl single crystal grown from melt
Lyasnikova M.S., Kylishov A.A., Yurasik G.A., Karimov D.N., Postnikov V.A., Voloshin A.E.
Abstract

The results of the study of the photoluminescent and X-ray luminescent properties of the p-terphenyl crystalline element made from a single crystal grown from a melt using the Bridgman method are presented. The transmission, photoluminescence and X-ray luminescence spectra of the crystals were obtained and analyzed. The kinetics of photoluminescence and X-ray luminescence decay have been studied for p-terphenyl single crystal and the absolute light yield of X-ray luminescence has been determined.

Kristallografiâ. 2024;69(6):1004-1008
pages 1004-1008 views
Atomistic simulation of paratellurite α-teo2 crystal: i. Defects and ionic transport
Ivanov-Schitz A.K.
Abstract

The structure and defects of α-TeO2 paratellurite crystals have been studied using computer modeling. It has been shown that in α-TeO2 the preferred point defects are oxygen vacancies and interstitial oxygen ions. Oxygen vacancies can be either isolated or form complex clusters. It is energetically most favorable for interstitial oxygen ions to be located in channels that penetrate the paratellurite structure along the c-axis. The origin of possible oxygen–ion transport in α-TeO2 is discussed.

Kristallografiâ. 2024;69(6):1009-1017
pages 1009-1017 views
Plasmon polaritons of the TE and TM types in a metal film bordering a superlattice I. Properties of impedances of half-infinite media and films
Darinskii A.N.
Abstract

A theoretical investigation is conducted into the behaviour of TE and TM-polarised surface plasmon polaritons in a metal film situated between a periodic superlattice and a homogeneous dielectric, or alternatively, between two periodic superlattices. The dispersion equations are derived in the form of the determinant of a real symmetric matrix equalling zero. The matrix is constituted by the surface impedances of the media and the film. A number of general properties of the impedances and eigenvalues of the matrices entering the dispersion equations are established.

Kristallografiâ. 2024;69(6):1018-1028
pages 1018-1028 views
Plasmon polaritons of the TE and TM types in a metal film bordering a superlattice II. analysis of the existence of plasmon polaritons
Darinskii A.N.
Abstract

The maximum number of TE and TM polarised surface plasmon polaritons in the forbidden zone of the Bloch spectrum of electromagnetic waves in a periodic superlattice is established in structures containing a metal film between a homogeneous medium and a periodic superlattice or between two superlattices. It is demonstrated that the determining factor in the maximum number of such waves is the type of frequency dependence of the superlattice impedance. Moreover, the maximum number of surface plasmon polaritons is contingent upon the structural type and polarization of the wave.

Kristallografiâ. 2024;69(6):1029-1036
pages 1029-1036 views

НАНОМАТЕРИАЛЫ, КЕРАМИКА

Bi nanostructures obtained on Si substrates by thermal evaporation method
Kozhemyakin G.N., Kiiko S.A., Kiiko A.V., Artemov V.V., Volchkov I.S.
Abstract

Bi low dimensional structures were obtained on the Si(100) substrates by thermal evaporation method in Ar. Bi nanocrystals and nanowires were condensed on the Si substrates at 10–20 s deposition time. Computer processing of SEM-images was used to determine the sizes of Bi nanocrystals and microcrystals and their distribution densities. The distribution density of nanocrystals was larger than its the microcrystals by a factor of 85–260. The increase of deposition time up to 20 s reduced the nanocrystal density by a factor of 2 with the increase of their sizes. X-ray diffraction analysis revealed oxide layers on the Bi nanocrystals and the Si substrates. The decrease in the sizes of the Bi nanocrystals and the increase in their density on the Si substrates in comparison with those on glassy carbon substrates were observed.

Kristallografiâ. 2024;69(6):1037-1043
pages 1037-1043 views

CRYSTAL GROWTH

Crystals of 4,7-bis(2,5-dimethyl-[1,1'-biphenyl]-4-yl)benzothiadiazole and Its Derivative with Terminal n-Hexyl Substitutes: Growth, Structure, Thermal and Absorption-Fluorescent Properties
Postnikov V.A., Sorokina N.I., Yurasik G.A., Сорокин Т.А., Kylishov A.A., Lyasnikova M.S., Popova V.V., Svidchenko E.A., Surin N.M., Borshchev O.V.
Abstract

This study presents an investigation into the crystallization and absorptive-fluorescent properties of linear conjugated molecules derived from 2,1,3-benzothiadiazole, specifically 4,7-bis(2,5-dimethyl-[1,1'-biphenyl]-4-yl)benzothiadiazole (Ph-Xy-BTD) and 4,7-bis(4'-hexyl-2,5-dimethyl-[1,1'-biphenyl]-4-yl)benzothiadiazole (Hex-Ph-Xy-BTD). The synthesis of a new derivative of Hex-Ph-Xy-BTD is described. It was found that the presence of terminal n-hexyl substituents in Hex-Ph-Xy-BTD leads to a lower melting point, increased solubility and has a positive effect on crystallization compared to Ph-Xy-BTD. Single crystals of Hex-Ph-Xy-BTD were grown from hexane solution, and their structure was elucidated using single-crystal X-ray diffraction, confirming a monoclinic system (space group P21/c, Z = 4). Absorption and fluorescence spectra were obtained and analyzed for solutions in tetrahydrofuran as well as for the crystals of Ph-Xy-BTD and Hex-Ph-Xy-BTD, alongside investigations of quantum yield and fluorescence lifetime.

Kristallografiâ. 2024;69(6):1044-1055
pages 1044-1055 views

КРИСТАЛЛОГРАФИЧЕСКИЕ МЕТОДЫ В ГУМАНИТАРНЫХ НАУКАХ

Comprehensive studies of sarmatian pendant mirrors
Antipenko A.V., Smekalova T.N., Kulikov A.V., Fridrichson S.K., Loboda A.Y., Guryeva P.V., Kovalenko E.S., Tereschenko E.Y., Yatsishina E.B.
Abstract

This study considers the elemental composition and manufacturing technology of mirrors of the so-called Sarmatian type. The examined mirrors are fortuitous discoveries originating from the territory of the Kerch Peninsula. All three objects are pendant mirrors with radial-beam ornamentation, which appeared at the turn of the 1st and 2nd centuries AD and existed until the beginning of the 3rd century AD. The results of X-ray fluorescence analysis of the alloy composition indicate that the mirrors are made of an alloy of copper, tin and lead with similar qualitative characteristics. The method of X-ray tomography clarified the details of the relief ornamentation, which was poorly expressed on the items due to corrosion.

Kristallografiâ. 2024;69(6):1056-1061
pages 1056-1061 views
Attic polychrome figured vessels from the state historical museum: comprehensive studies
Zhuravlev D.V., Ilyina T.A., Tereschenko E.Y., Guryeva P.V., Kovalenko E.S., Kondratyev O.A., Kuzmina E.A., Kulikova E.S., Mandrykina A.V., Shaliavina N.B., Yatsishina E.B.
Abstract

This article presents the results of comprehensive studies of three Attic figured vessels from the 4th century BC, drawn from the State Historical Museum collection. The application of X-ray tomography, large-scale XRF mapping, energy-dispersive X-ray microanalysis under SEM and synchrotron XRD analysis enabled a comprehensive examination of the vessels' state of preservation, including the identification of restoration traces and the delineation of the manufacturing technology employed. Additionally, the analysis facilitated the identification of the pigments utilized in the surface painting. A reconstruction of the polychrome painting of the vessels was proposed based on the pigment residues identified both visually and on XRF maps. Given the poor state of preservation of the coating on the surface of two vessels, a reconstruction of their possible polychrome painting was performed based on a comparison with known analogues.

Kristallografiâ. 2024;69(6):1062-1077
pages 1062-1077 views
On the technology of production of antique red-glazed pottery (bosporan, pontic and eastern sigillata)
Mandrykina A.V., Zhuravlev D.V., Guryeva P.V., Kovalenko E.S., Kondratyev O.A., Khmelenin D.N., Tereschenko E.Y., Yatsishina E.B.
Abstract

A comprehensive study of antique red-glazed pottery fragments (terra sigillata) belonging to the Pontic, Bosporan and Eastern groups has enabled the identification of distinctive technological characteristics of the slip layer and ceramic mass. The Eastern sigillata samples exhibited superior technological characteristics. The small size of the pores and inclusions is indicative of the utilisation of finely dispersed clay. Furthermore, the presence of a mixture comprising two distinct clay types was identified: a ferrous clay and a more refractory calcareous clay. The particular and likely meticulous preparation of the clay suspension for the slip layer production was indicated by the addition of a potassium-containing preparation, presumably potassium potash, to enhance the glazing of the layer, as well as an iron-containing pigment, probably ocher. The samples were fired at a temperature of approximately 1000°C. Pontic sigillata products were distinguished by the addition of potassium potash in accordance with Eastern techniques and the absence of a specially added pigment in the varnish mixture. The firing temperature was lower, falling within the range of 850–900°C.

Kristallografiâ. 2024;69(6):1078-1089
pages 1078-1089 views
Construction solutions of the eski-kermen and gorzuvit tombs
Loboda A.Y., Kalinin P.I., Antipin A.M., Guryeva P.V., Kovalenko E.S., Mandrykina A.V., Kuzmina E.A., Khairedinova E.A., Mastykova A.V., Tereschenko E.Y., Yatsishina E.B.
Abstract

A comparative analysis of the mortars used in the construction of two burial structures in medieval Crimean cities, namely Eski-Kermen and Gorzuvit, was conducted. In both instances, lime mortar was employed. The faunal remains discovered within the lime base enabled the origin of the carbonate raw material to be determined. In the case of Eski-Kermen, the lime mortar was prepared from Eocene nummulitic limestone, which constitutes the plateau itself. In contrast, the limestone of the Upper Oxfordian deposits of the southern slopes of the Main Ridge of the Crimean Mountains was used in Gorzuvit. As technological admixtures in Gorzuvites, rounded large pebbles (of river or sea origin), sand, presumably of river origin, and plant remains were employed. On the Eski-Kermen plateau, due to the limited availability of resources, mainly only heterogeneous, fairly large fragments of crushed, partially burnt ceramics were used. The obtained results confirm the hypothesis that local changes in the formulation of solutions are associated with the availability of raw materials near the construction site, both natural and anthropogenic.

Kristallografiâ. 2024;69(6):1090-1100
pages 1090-1100 views