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Journal of Structural Chemistry

2014 year, number 1

1.
UNIVERSALITY OF CRYSTALLOGRAPHY

S. F. Solodovnikov1,2
1Nikolaev Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
Keywords: crystallography, crystal chemistry, history, crystal structure, structural design, structural chemistry

Abstract >>
The work briefly considers the historical development of crystallography from a "servant of mineralogy" to a basis of the modern natural sciences, which became possible thanks to the discovery, in 1912, of the diffraction of X-rays by crystals and X-ray structural analysis with the subsequent rapid accumulation of structural knowledge in chemistry and other sciences.
																								



2.
ROLE OF RUSSIAN SCIENTISTS IN THE DISCOVERY OF X-RAY CRYSTALLOGRAPHIC ANALYSIS IN THE BEGINNING OF THE SCIENTIFIC REVOLUTION OF THE 20TH CENTURY

V. S. Urusov
Lomonosov Moscow State University, Moscow, Russia
Keywords: discovery of Laue, basics of X-ray crystallographic analysis, works of L. and H. Braggs, works of Vulf, crystalline lattice symmetry, works of Fedorov

Abstract >>
In connection with the 100th anniversary of the discovery of the phenomenon of the diffraction of X-rays by crystals (Max von Laue, 1912) and the basics of X-ray crystallographic analysis (Lawrence Bragg, 1913), the article marks the major milestones in this outstanding event in the history of science. Special emphasis is given to the role of Russian scientists (E. S. Fedorov, G. V. Vulf) in the emergence and early steps in the establishment of this discovery being one of the pillars of the scientific revolution of the first half of the past century.
																								



3.
ANALYSIS OF LAUE PATTERNS: ONE CENTURY AFTER

V. M. Pugachev
Kemerovo State University, Kemerovo, Russia
Keywords: X-ray diffraction, Laue method, Laue pattern, zone, single crystal, zone axis, crystallographic direction

Abstract >>
Several formulae are suggested allowing the measurement of angles between the primary X-ray beam and the zone axes. This makes it possible to derive a single crystal lattice and determine its orientation from a single Laue photograph.
																								



4.
THE TECHNIQUE OF X-RAY DIFFRACTION INVESTIGATION OF CRYSTAL AGGREGATES

A. V. Panchenko1,2, N. D. Tolstykh3, S. A. Gromilov1,2
1Nikolaev Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
3Sobolev Institute of Geology and Mineralogy, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
Keywords: X-ray diffraction, Debye-Scherrer method, CCD detector, minerals

Abstract >>
A number of experimental techniques of the X-ray diffraction investigation of crystal aggregates is presented with employment of modern diffractometers equipped with 2D CCD detectors. Fundamentally, these techniques are based on taking a series of Debye-Scherrer photographs. The measurement accuracy of the interplanar distances and unit cell parameters using internal and external standards is discussed.
																								



5.
ROLE OF BOUND WATER AND PRECIPITANTS IN THE SELF-ORGANIZATION OF BIOCRYSTALS

N. A. Bulienkov, E. A. Zheligovskaya
Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
Keywords: protein crystals, bound water, modular design

Abstract >>
It is shown that the unit cell parameters of biocrystals can be expressed as the sum of the pseudoperiods of a 30/11 helix composed of water molecules, which is the main element in the structure of the hydration shells of biocrystals. It is suggested that bound water molecules in the structure of a biocrystal form a lattice with edges that are essentially 30/11 helices spaced at a distance of the length of the corresponding pseudoperiod. An account is given of the role of precipitant in stabilizing this lattice. The conclusions are used to explain the polymorphism of biocrystals and the possible existence of large cavities and wide through channels in the structures of biocrystals in the case of polyethylene glycol and similar molecules of the corresponding length being used as a precipitant.
																								



6.
TO THE FORMATION OF AGGREGATE STRUCTURES OF KIDNEY STONES

A. R. Izatulina1, Yu. O. Punin1, O. A. Golovanova2
1St. Petersburg State University, St. Petersburg, Russia
2Dostoevsky Omsk State University, Omsk, Russia
Keywords: calcium oxalate monohydrate, aggregation, kidney stones

Abstract >>
The work considers the aggregation process of calcium oxalate monohydrate crystals (whewellite) during their crystallization from aqueous solutions. The intensive crystal aggregation during the precipitation is evidenced by a decrease in the bulk concentration against an increase in the crystal size. At the initial stages of crystallization fine particles are mainly captured by larger ones in the form of substance deposition on the initiating centers: organic blobs, dead cells, and so on. During the crystallization the effect of the dominant growth of large aggregates increases; the process develops autocatalytically; fine particles disappear more rapidly than large ones, and the crystal size distribution compresses simultaneously with an increase in the average particle size.
																								



7.
CRYSTALLOGRAPHY OF SULFIDES: COMPOSITION AND SYMMETRY VARIATIONS

S. V. Borisov, S. A. Magarill, N. V. Pervukhina
Nikolaev Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
Keywords: crystallographic analysis, symmetry of sulfide structures, cationic and anionic "skeletons", Tl cation in sulfides

Abstract >>
The factual material obtain in a crystallographic study of sulfides is used to show the role of symmetry in the formation of structures. Note is made of the fundamental contribution of mirror symmetry planes to the architecture of sulfide structures since they reveal the common basis, or common "gene", of these structures. Concrete examples are employed to analyze the genetic link between the popular structural types of sulfides. An account is given of the features of autonomous ordering in cationic and anionic matrices and the role of the big Tl cation in these processes.
																								



8.
STRUCTURAL EVOLUTION OF MICROPOROUS ZIRCONOSILICATE ELPIDITE UNDER HIGH PRESSURE

Yu. V. Seryotkin1,2, V. V. Bakakin3, I. V. Pekov4
1Sobolev Institute of Geology and Mineralogy, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
3Nikolaev Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
4Lomonosov Moscow State University, Moscow, Russia
Keywords: zirconosilicate, elpidite, crystal structure, high pressure, phase transitions

Abstract >>
A high-pressure (up to 4.95 GPa) single-crystal XRD study is carried out of the natural zeolite-like hetero-framework zirconosilicate elpidite |Na1,65Ca0,15(H2O)3| [ZrSi6O15], sp. gr. Pbcm, a = 7.13201(19) Å, b = 14.6787(4) Å, c = 14.6297(3) Å, V = 1531.56(7) Å3, Z = 4. At pressures above 1.2 GPa, the elpidite undergoes a phase transition with the doubling of the a parameter of the unit cell (sp. gr. Pbca). The transition is caused by the opposite rotation of the originally equivalent Zr octahedra. Above 3.5 GPa, another phase transition is detected, this time with the symmetry being reduced to monoclinic (sp. gr. C1121/a). The framework deformation leads to a partial reorientation of H bonds in the extra-framework subsystem and a change in the configuration of Na and H2O chain from a unilaterally branched pattern to a bilaterally branched one.
																								



9.
MORPHOTROPISM, POLYMORPHISM AND BEHAVIOR ON HEATING OF ODD MONOCARBOXYLIC ACIDS CnH2nO2 IN THE HOMOLOGOUS SERIES n = 11–21

Y. M. Trushkina, E. N. Kotel'nikova
St. Petersburg State University, St. Petersburg, Russia
Keywords: monocarboxylic acids, odd fatty acids, polymorphism, morphotropism, thermal phase transitions, express test, powder X-ray diffraction, variable temperature X-ray diffraction

Abstract >>
X-ray diffraction characteristics are obtained for odd monocarboxylic acids (fatty acids) CnH2nO2 with n = 11, 13, 15, 17, 19, and 21. It is found that all original samples (reagents) of these acids are two-phase. There are found the following modifications: for the acid with n = 11 triclinic Tc (space group P–1) and monoclinic M3 (space group P21/c); for n = 13 triclinic Tc (space group P1) and bilayered monoclinic 2 M (space group A2/ a); for n = 15, 17, 19, 21 two monoclinic M1 (space group P21/a) and M3 (space group P21/). It is demonstrated that the homological series and individual homologues of fatty acids manifest noticeable crystal chemical features such as morphotropism and polymorphism, respectively. Thermal phase transformations of odd fatty acids are studied using pentadecanoic acid C15H30O2 as a representative example. It is found that near the melting point (52 °C) within the temperature range of 4550 C the monoclinic phase M1 of this acid undergoes a polymorphic transformation in the high-temperature bilayered monoclinic phase 2 . The data obtained are compared to those reported in the literature. An express standardless test is developed for the determination of homologues (the n value) and polymorphic modifications of monocarboxylic acids.
																								



10.
CATION ORDERING AND STRUCTURAL DEFORMATIONS IN PECTOLITE HNaCaSi3O9 – SERANDITE HNaMn2Si3O9

I. V. Rozhdestvenskaya1, V. A. Vasilieva2
1St. Petersburg State University, St. Petersburg, Russia
2Karpinskii All-Russian Research Geological Institute, St. Petersburg, Russia
Keywords: pectolite, serandite, single crystal X-ray analysis, isomorphism

Abstract >>
Using the X-ray diffraction analysis, the structures of the pectolite-serandite series with the general formula HNaCa2–xMnxSi3O9, are studied where 0 < x < 2, with x = 0.02, 0.14, 0.39, and 1.17. The Mn2+ cations mostly occupy the M2 site (0.02, 0.14, 0.34, and 0.90 apfu). Here <M1O> = 2.3672.369 Å decreases down to 2.355 Å; <M2O> decreases from 2.355 Å to 2.239 Å. The lengths 34 = 2.472.49 Å, bond lengths HO3 = 1.071.24 Å and HO4 = 1.441.32 Å. For <M1O> and <M2O> of about (Mn2+ + Fe2+) ≈ 1 a turning point is noted in the graph. The a, b, c, and β parameters decrease linearly.
																								



11.
TERMS OF PARITY AND DISTORTION OF COORDINATION POLYHEDRA IN INORGANIC CRYSTAL CHEMISTRY

V. S. Urusov
Lomonosov Moscow State University, Moscow, Russia
Keywords: coordination polyhedra, stability, distortion theorem, increased distribution dispersions

Abstract >>
The coordination number parity law is formulated: the coordination polyhedra (CP) with the odd number of vertices, except for 3 (CP is a triangle), occur far less often than the polyhedra with the even number of vertices. CP with the odd number of vertices, except for the triangle, cannot be regular and have at least two different types of vertices and two sets of interatomic lengths. The main and first c.n. always keeps parity. A CP distortion due to crystal chemical causes tends to be minimum, obeying the pseudo-symmetry laws. A CP distortion, other things being equal, leads to an increase in the average bond length as compared to the regular polyhedron (distortion theorem). The value of the increase in the average interatomic distance depends on the degree of distortion by the linear or (for a very strong distortion) the square dependence. The histograms of the distribution frequencies of the interatomic lengths have a positive deviation from the Gauss normal distribution law. A free molecule or a complex ion having a distortion due to the directed configuration of chemical bonds or to the electronic effects of the Jahn–Teller type for transition metals, maintain it in the crystal structure as well. During the polymerization of radicals there arise specific distortion effects due to a various coordination environment of the bridging and apical ligands. One of the most general rules of the CP distortion is associated with a less symmetric and less homogenous environment of anions in comparison with that of cations and a higher polarizability of anions. An important exception from this rule is the group of compounds with the so called anioncentered tetrahedra in which more symmetrical positions are occupied, as a rule, by anions in the center of the tetrahedra.
																								



12.
E. S. FEDOROVS ALGORITHM OF THE GENERATION OF THE COMBINATORIAL DIVERSITY OF CONVEX POLYHEDRA: THE LATEST RESULTS AND APPLICATIONS

Yu. L. Voytekhovsky
Geological Institute, Kola Scientific Center, Russian Academy of Sciences, Apatity, Russia
Keywords: convex polyhedron, combinatorial type, Fedorovs algorithm, point symmetry group, crystallographic and non-crystallographic symmetry groups, combinatorially asymmetric polyhedra, Schlegel projection, systematic and nomenclature of convex polyhedra

Abstract >>
E. S. Fedorov’s algorithm allowing us to obtain the full combinatorial diversity of convex polyhedra from the tetrahedron is considered in the paper. The latest results on the number of combinatorially different convex n–hedra for the given n and their point symmetry groups are presented. Possible applications of the results are shown. The problems are formulated, which can be solved at present only by means of powerful computers.
																								



13.
INTERPENETRATION OF THREE–PERIODIC NETWORKS IN CRYSTAL STRUCTURES: DESCRIPTION AND CLASSIFICATION METHODS, GEOMETRICALTOPOLOGICAL CONDITIONS OF IMPLEMENTATION

E. V. Alexandrov1, V. A. Blatov1, D. M. Proserpio2
1Samara State University, Samara, Russia
2University of Milan, Universita' degli Studi di Milano, Via Golgi, 19 - 20133 Milano, Italy
Keywords: interpenetration, topological analysis of atomic networks, cavity sizes, channel sizes, architecture of cavities and channels, stereochemistry

Abstract >>
This review describes the current state of studies on the phenomenon of interpenetration of framework groups in crystal structures. The generally accepted terminology used in the description of topology of interpenetrating motifs, symmetric and topological properties of interpenetrating systems is given. The main advances of crystal chemistry in the systematization of interpenetrating structures are elucidated. It is noted that the major trend in the crystal chemistry of interpenetration is the development of methods for the topological classification of the entanglements of interpenetrating groups and the search for the regularities of their implementation in crystalline substances. The main ways of the formation of interpenetrating structures, the appearing here geometrical-topological restrictions, and also the effect of stereochemical factors and synthesis conditions on the possibility of interpenetration are considered.
																								



14.
THERMAL DECOMPOSITION OF LAYERED DOUBLE HYDROXIDES Mg–Al, NiAl, MgGa: STRUCTURAL FEATURES OF HYDROXIDE, DEHYDRATED, AND OXIDE PHASES

N. N. Leonteva1, S. V. Cherepanova2,3, V. A. Drozdov1
1Institute of Hydrocarbons Processing, Siberian Branch, Russian Academy of Sciences, Omsk, Russia
2Boreskov Institute of Catalysis, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
3Novosibirsk State University, Novosibirsk, Russia
Keywords: X-ray diffraction, hydrotalcite, mixed oxide, disordered structure, stacking faults

Abstract >>
The analysis of the literature data reveals that, as a rule, layered double hydroxides prepared by co-precipitation have an imperfect structure; however, there are different viewpoints on the type of the defects. Thermal decomposition of Mg–Al, MgGa, and NiAl hydroxides occurs through dehydration, dehydroxylation, and decarbonization. The first stage affords a layered dehydrated phase with a strongly disordered structure, which is a subject of controversy. Also, the question on the diffusion of cations during thermolysis is still open, i.e., whether the MgAl, MgGa and NiAl systems degrade with the development of a nanoheterogenous oxide systems or a single-phase mixed oxide, but with very defective structure, is formed.
																								



15.
CRYSTALLOGRAPHY AND HIGH–TEMPERATURE CRYSTAL CHEMISTRY OF ANHYDROUS BOROSILICATES OF ALKALI AND ALKALIEARTH METALS

M. G. Krzhizhanovskaya1, R. S. Bubnova1,2, S. K. Filatov1
1Department of Crystallography, St. Petersburg State University, St. Petersburg, Russia
2Institute of Silicate Chemistry, Russian Academy of Sciences, St. Petersburg, Russia
Keywords: borosilicates, silicoborates, crystal chemistry, polymorphism, thermal expansion

Abstract >>
The crystal structures and thermal behavior of anhydrous borate-silicates of alkali and alkali-earth metals are briefly overviewed. In silicoborates (B/Si > 1), the boron atoms occur in triangle and tetrahedral coordination, as in borates; in two of three known silicoborates, the unique layered and chained polyanions are found. The known borosilicates (B/Si ≤ 1) have a framework structure formed from tetrahedrally coordinated atoms of boron and silicon; some borosilicates belong to the known structural types of aluminosilicates, while the others are only structurally similar to them and silica modifications, whereas their tetrahedral frameworks are topologically identical to that of aluminosilicates and SiO2. The exception are borosilicates Li4B4Si8O24 and lisitsynite KBSi2O6, having the original frameworks. In line with the similarity of chemical composition and commonality of crystal structure, thermal behavior of borosilicates appears to be similar to that of aluminosilicates and silicates, however, borosilicates have considerably lower temperatures of formation, polymorphic transformations, and melting.
																								



16.
CRYSTALLIZATION OF CALCIUM OXALATE MONOHYDRATE IN THE PRESENCE OF AMINO ACIDS: FEATURES AND REGULARITIES

O. A. Golovanova1, Yu. O. Punin2, A. R. Izatulina2, V. V. Korol'kov1
1Omsk State University, Omsk, Russia
2St. Petersburg State University, St. Petersburg, Russia
Keywords: kidney stones, crystallization and nucleation kinetics, protein constituent, amino acid composition, calcium oxalate monohydrate

Abstract >>
The protein composition of the organic component of kidney stones and the effect of major amino acids of the physiological solution on the crystallization process of calcium oxalate is studied in the work. By means of a complex technique the protein compounds are analyzed in 40 samples of kidney stones obtained by both direct surgical operations and distant lithotripsy. A strong and selective concentration of amino acids in different stones in comparison with the physiological fluids forming them is established. Nucleation processes and the crystallization kinetics of calcium oxalate monohydrate are studied in the model solutions without impurities and with additions of 13 amino acids. Different amino acids can both inhibit and promote these processes depending on the acid structure.