Home – Home – Jornals – Journal of Structural Chemistry 2009 number 7

We propose new algorithms to generate (predict) the structures of molecular crystals, which are based on the method of discrete modeling of molecular packings. We consider the specific features of generation algorithms for homomolecular and some heteromolecular compounds. We also study the possibility to use these algorithms for interpreting X-ray diffraction experiment.

Different growth models of crystal structures are briefly considered. A metric model of layer-by-layer sectoral growth proposed in [1] is described along with its application for computer modeling of the assembly of nanosized crystal growth nuclei by clusterizing the unit cell content.

Using Voronoi-Dirichlet polyhedra, the principle of maximum space filling in sublattices containing atoms of a particular element (from H to Cf) is tested in the structures of all crystalline compounds studied so far. It is found that atoms of the overwhelming majority of elements are most often surrounded by 14 neighboring atoms in these sublattices. Anomalous features of H- and C-sublattices, in which hydrogen and carbon atoms most commonly have 15 and 16 neighboring atoms respectively, and sublattices consisting of Ar, Ac, Pa, Am, Cm, Bk, or Cf atoms, in which the number of nearest neighboring atoms is usually 12, are discovered. The main reasons for the revealed differences are discussed.

Statistical analysis of modern structural databases on inorganic crystals and minerals is carried out to elucidate the classification of crystal structure distributions over space groups. The known fact about extremely uneven occupation of space groups is confirmed; the relative abundance of all and, in particular, 24 most frequent groups (>1%) is derived, and the latter are noted to belong to holohedral and centrosymmetric classes. The data on occupation of extremely rare and empty space groups are analyzed and refined separately, which allows the reduction of a number of unreliable structural data. The theoretical analysis of empirical regularities is performed from the standpoint of filling rules for special structural positions (Wyckoff positions) and the symmetry of lattice complexes. It is shown that only combined consideration of different symmetry rules and restrictions provides an explanation for most regularities observed in occupation of symmetry point groups.

The paper describes G. B. Bokii's idea of separating the primary classification levels of the mineral world and the results of developing the database containing G. B. Bokii's decimal symbols.

Formulas of the local coordination of vertices and faces of simple and dual forms, solids of Plato, Archimedes, Hessel, and Fedorov, Kepler-Shubnikov and Laves nets, maps of potentials and zeolite nets, models of crystal nuclei are presented. All the obtained formulas enter the arrays determined previously. Alphabet formulas of ligand sequences contain no more than 1-7 different letters. The revealed formula sets predetermine the stability of a small number of qualitative and quantitative relations in multi-scale systems and the similarity of local coordination in the ordering and disordering.

The role of crystal chemical factors in the development of conditions for the formation of the magnetic structure of inorganic compounds is shown. A crystal chemical method is proposed to quantitatively estimate the strength of magnetic interactions and to determine magnetic moment orientation based on the structural data. By the example of determining the magnetic structures of two known antiferromagnetics Cs₂CuCl₄ and Sr₂CuO₃ the correspondence between the results obtained by this method and the experiment is shown. It is found that the search for new materials with the sought magnetic structure can be made using the data on the crystal structure of compounds. New Tl₂Cu(CO₃)₂, BaCu₂(AsO₄)₂, BaV₂P₂O₁₀, VOSe₂O₅, KCu(CO₃)F, and A(VO)(XO₄) (A = Li, Na, NH₄, K; X = P and As) magnets containing low-dimensional fragments are found. Magnetic interactions are analyzed; based on the structural data, the sign and strength of magnetic interactions is calculated both inside the low-dimensional fragments and between them; geometrical frustrations are studied in all compounds found.

The work considers the structural features of condensed phases under negative pressures that can be implemented under all-round stretching. It results in a decrease in the phase density due to an increase in interatomic distances, the appearance of structural defects, and the formation of new low density structures. It is noted that the stretched states are also characteristic of metastable phases such as liquids, glasses, and loose crystal structures in the region of positive pressures.

Based on structural studies of Sr_xBa_1-xNb₂O₆ crystals with different concentrations of strontium and barium, the structural causality of optical nonlinearity of these crystalline materials is established. YAG:Nd laser radiation of the crystals results in a monotonic decrease in the second harmonic intensity with increasing strontium concentration in a sample. Fine details of the structure responsible for this effect are determined.

Different approaches to the individualization of mineral species formulated by G. B. Bokii and his opponents are considered. It is shown that with the development of techniques of X-ray experiments the "dominance principle" used in structural chemistry became the main tool in discovering new minerals. On the example of the eudialyte group, the individualization of mineral species distinguished by chemical and structural features, physical properties, and formation conditions is demonstrated.

Crystal chemical features of some complex oxide lithium-containing compounds, in particular, triple molybdates, are considered to reveal the structure-forming significance of lithium. Its role is actually reduced to the realization of structures with a simpler composition through the introduction and heterovalent substitution. Specific stabilization ways can be very diverse owing to the high adaptability of lithium atoms in the structure. They can reside in the same crystallographic positions together with alkali metals (including potassium), medium-size, and even larger two- and three-charged cations and also to occupy the cavities. Such an adaptability and a low charge of the Li⁺ ion with its appropriate distribution in the structure allow the elimination of imbalance in cation charges and sizes of their coordination polyhedra. They also provide the filling of available vacancies, which produces a significant stabilizing effect. The stabilization of the structures with other cations or their combinations is exemplified. Attention is drawn to the relation between the structural and thermal stabilization. It is concluded that the crystal chemical stabilizing features of lithium and other cations can be used as an instrument for the design of novel compounds and materials.

A model crystalline approximant of the surface layer (SL) structure of liquid mercury is formed using the algorithm, previously applied to form a crystalline approximant of the SL structure of water, the experimental data on the SL structure of mercury, and the stereochemical data for Hg atoms in the α-Hg crystalline phase and bulk liquid mercury. The correspondence of the metrics of the crystalline approximant proposed for the SL structure of mercury and Langmuir monolayers composed of organic molecules with hydrocarbon tails and different hydrophilic groups on liquid mercury to the position of molecules along mercury SL is shown.

The main theoretical principles of the fragment model are presented. It is shown that in constructing the model radial distribution functions of atoms the parameters of the experimental radial distribution function are not used, and the model can be used to identify diffraction amorphous nanodispersed materials, to analyze the atomic structure of classic glasses, and also in the phase analysis of amorphous materials. The procedure is easy to use and does not require cumbersome calculations; the necessity to perform relaxation is absent.

The application of high pressure techniques that stimulated the development of inorganic crystal chemistry, provided the discovery of new types of polymorphic transformations, showed the insufficiency of the ionic model to describe the crystal structures of even binary compounds, poses some unexpected theoretical questions.

The geometry of cation and anion matrices is analyzed in the crystal structures of complex sulfides with the symmetry mirror planes perpendicular to the short translation of ~4 Å. In support of the developed crystalline state concept, the structures exhibit the spatial atomic ordering by the systems of crystallographic planes. This includes the absolute ordering by the symmetry mirror planes that tend to form hexagonal sublattices with trigon 3⁶ nets.

Crystal chemical analysis of natural clay material that formed under different physicochemical parameters shows that the analyzed samples are represented in series I by almost pure smectite (K,Na,Mg,Ca)_x·nH₂O·(Fe,Mg)₂(Si,Al,Fe)₄О₁₀(OH)₂, in series II by smectite with a small impurity (~15%) of quartz (SiO₂) and plagioclase (NaAlSi₃O₈/CaAl₂Si₂O₈). The studies are performed by X-ray diffraction, IR spectroscopy, electron microscopy, and microprobe analysis. It is shown that the values of d₀₀₁ basal reflections of the smectites in question within 11-13 Å are due to the degree of cation occupation and hydration of the interlayer space, and differences in the frequencies of IR spectra are caused by isomorphic substitutions in the structure. Microprobe analysis results, calculated crystal chemical formulas, and values of b parameters are held only for the extreme terms in a series of dioctahedral ferric smectites: nontronites. The results reveal differences both in the composition, structure, properties, morphology and IR spectroscopic characteristics of nontronites of different origin.

Formulas of natural zeolites are generally cumbersome and not easily comparable because of differences in their written form. A summary of the formulas normalized at n = 1 is given for aluminosilicate zeolites with the [(Si,Al)_nO_2n] frameworks. Novel volume parameters are proposed for the framework instead of the framework density (FD) and a zeolite as a whole, which are calculated as the effective volumes of a mean (Si, Al, O) atom and a mean atom of the compound. We show the efficiency of the comparative crystal chemical analysis of zeolites in a common scale with the use of unified characteristics.

A systematic X-ray diffraction study of the interaction products of Zr(IV), Hf(IV), Nb(V), and Ta(V) oxides (fluorides) with crown-ethers (CEs) in aqueous solutions of hydrofluoric acid is performed. It is shown that oxygen-containing CEs form oxonium complexes with [NbF₆]^- and [TaF₆]^- hexafluorometallate anions. In two systems, [cis-syn-cis-DCH18C6·H₃O][TaF₆] and [B18C6·H₃O][TaF₆], the phenomenon of supramolecular isomerism is found, which is caused by a change in the conformation of the macrocycle or by a partial redistribution of intermolecular hydrogen bonds. The use of aza-crown ethers as extractants made it possible to extract unique hydrolytically unstable anions, the products of incomplete fluorine substitution for oxygen atoms in the starting oxides in the form of crystalline complexes with a composition of [(HA15C5)₂][Ta₂F₁₀O] and [(HA18C6·H₂O)(A18C6·H₂O)] [(H₂O)Nb₂F₉O]. In [(18C6)(H₇O₃)₂∙(Hf₂F₁₀·2H₂O)], [(HA18C6)(M₂F₁₀·2H₂O)·(H₃O)·H₂O], and [(H₂DA18C6) (M₂F₁₀·2H₂O)·2H₂O] (M = Zr, Hf) complexes, the metals are extracted in the form of identical (M₂F₁₀·2H₂O)^2- anions with a similar topology. The performed study demonstrates that macrocyclic complexones are undoubtedly promising to extract Zr(IV), Hf(IV), Nb(V), and Ta(V) from fluorine-containing aqueous solutions.

The results of studies on the structure of organic complexes of the derivatives of 1,3-dihydropyrimidine-2,4-diones and their structural analogues with macrocyclic poly- and azapolyethers are generalized.

The article summarizes the results of the study of conformational states of triosmium clusters with organic ligands. Special attention is paid to the structural features of molecular carbonyl cluster complexes with M_n(CO)_mL organic ligands. The effect of the structure surface charge, solvent, cluster crystalline state, and intermolecular and intramolecular interactions on the cluster conformational state is also determined.

We analyze the specific features of the structure and properties of crystals that belong to the family of low-dimensional molecular conductors based on BEDT-TTF (ET) radical cation salts with [MNOX₅]^2- (M = Os, Ru; X = Cl, Br) mononitrosyl metal complexes as anions. It is shown that when the synthesis components are changed single crystals with α′, β, δ, and κ-types of the conducting layers form. All radical cation salts of this family can be considered as pseudopolymorphous phases with a general formula of (ET)₄[MNOX₅]_2-xG_x (G is a guest solvent molecule, BN or NB). The studied crystals display a range of remarkable structural features such as conformational and charge ordering in the conducting ЕТ layers as well as commensurate and incommensurate structural modulations mainly related to the positional ordering of the components of complex anion layers.

The current development level of new crystal chemical methods connected with the topological analysis of atomic nets is briefly reviewed. The terminology used to describe atomic nets is considered along with the main methods for their classification and some special issues such as the study of interpenetrating nets and tilings. It is noted that the crucial problem of the modern crystal chemistry is the search for regularities underlying the global properties of a structure (both geometric and topological) such as the atomic net topology, types of atomic and molecular packing, size and architecture of voids and channels.

Results of studies performed under the guidance of A. E. Shvelashvili and continued after his decease are analyzed. We consider the coordination compounds containing both mono- and dihydrazides of carbonic acids; in particular, monohydrazides of monobasic benzoic and m-hydroxy benzoic acids (BH=C₆H₅C(O)NHNH₂, m-HBH=HOC₆H₅C(O)NHNH₂) and dihydrazides (DHs) of dibasic acids: malonic, succinic, and glutaric (DM=H₂NHN(O)C(CH₂)C(O)NHNH₂, DS=H₂NHN(O)C(CH₂)₂C(O)NHNH₂, and DG=H₂NHNOC(CH₂)₃CONHNH₂). Complex compounds of metals with carbonic acid hydrazides are grouped by the ratio between main components (M:Lig = 1:1 and M:Lig = 1:2) and by the gross formulas: M(Lig)XYnH₂O and M(Lig)₂XYnH₂O, where M(II) = Ca, Mn, Fe, Co, Ni, Cu, Zn, and Sr; Lig = ВН, m-HBH, DM, DS, DG, Х, Y (X, Y = Cl^-, NCS^-, I^-, Br^-, and are identical or different acido ligands, n = 0-4. The compounds with carbonic acid dihydrazides are classified by the redistribution criterion of ligands in the -M-DH-M- bonds depending on the M:DH ratio and the nature of the acido ligand. A division into two groups is performed by the criteria: 1) pairs of metal atoms with single bis-bidentate bridges; 2) pairs of metal atoms with double bis-bidentate bridges. Packing features of structural units are revealed in compounds containing residuals of carbonic acid hydrazides.

Intermolecular interactions in crystals of various azachalcagenenes with aromatic substituents, including polyfluorinated derivatives, are first analyzed and systematized. A topological analysis of crystal packing is carried out, and main supramolecular motifs are identified.