Crystal Structure Database Research Articles

Silanol groups in minerals and inorganic compounds

The Inorganic Crystal Structure Database (ICSD) was searched for Si-OH groups with ordered H positions leading to 31 structures with 46 Si-OH groups. The geometrical characteristics of these partly hydroxylated SiO 4 tetrahedra were analyzed. Depending on the condensation of the tetrahedra, the protonization of one tetrahedral apex allows variations in Si-O bond lengths and distorts the tetrahedron. The Si-OH distance decreases with the

Supergroups of space groups and their application to the prediction of structural phase transitions

A systematic procedure for the determination of supergroups of space groups is developed and used for the search of pseudosymmetric structures within crystal structure databases. The method is applied to P212121 structures listed in the Inorganic Crystal Structure Database. A significant number of compounds with known phase transitions at high temperatures are clearly detected as pseudosymmetric with differences between the transformed and original structure lower than 1·0 Å. Taking this value as a threshold about 20 additional compounds are detected having a high probability of exhibiting a phase transition at higher temperatures.

The hydride fluoride crystal structure database, HFD

HFD is a new data base containing crystal structure information on more than one thousand metal hydrides and fluorides. It includes space group, cell parameters, standardized atom positions, site occupancies and references. The compilation is critical as only refined crystal structures are considered and the data are checked for internal consistency. It is comprehensive as structural information is extracted from all major scientific journals, and it is continuously updated. HFD can be searched according to various criteria such as symmetry, chemical elements, composition etc. The primary motivation for creating HFD was to predict new metal hydrides and to study their structural analogies with metal fluorides. However, HFD can also be used for other applications such as the simulation of diffraction patterns and the drawing of crystal structures.

Application of exhaustive lattice match searches to the selection of epitaxial substrates for protein crystal growth

Software has been developed for exhaustive searches of crystal-structure databases to find all orientations of all known compounds that match the lattice of any plane of any desired epitaxial deposit. The program provides for screening by crystal symmetry, orientation, index and match range limits, type of compound, and mismatch tolerances. Since almost any search yields hundreds to thousands of candidate substrates, it has become necessary to develop screening procedures to reduce the large number of entries to a small list of available candidate materials with a reasonable likelihood of favorable results. The present paper concerns the particular problems involved in cases, such as protein crystal growth on inorganic substrates, where the unit parallelogram of the material to be deposited is far larger than those of the candidate substrates. These problems include selection of deposit and substrate orientations, types of lattice match, multiple-orientation lattice matches, feasibility of synthesis, and chemical/physical compatibility.

Zirconium dodecaboride, from the ICSD CD-ROM

Abstract The B12 unit of zirconium dodecaboride has been reported as an icosahedron according to the Inorganic Crystal Structure Data Base, whereas the reference work actually confirmed a cubeoctahedral arrangement for B12. Convergent beam electron diffraction was applied to verify the latter and original assignment.

Systematic search of materials with high-temperature structural phase transitions: Application to space group P212121.

The existence of a pseudosymmetry in a crystal structure is indicative of a slightly distorted structure of higher symmetry. If the distortion is small enough, it can be expected that the crystal acquires this more symmetric configuration at a higher temperature after a phase transition. The aim of the present study is the development of a general procedure for the systematic search of pseudosymmetric structures in the available structural databases. The first step is the determination of all relevant supergroups of the space group associated to the known structure. This problem is reduced to the generation of minimal supergroups of space groups using the existing data on their maximal subgroups and normalizers. The determined pseudosymmetry elements are then applied to the crystal structure and a quantitative comparison of the transformed structure and the original one is performed. Pseudosymmetry is detected when the difference is under a certain threshold. As an example we present the results obtained for inorganic structures with space group P${2}_{1}$${2}_{1}$${2}_{1}$ retrieved from the Inorganic Crystal-Structure Database. A significant number of compounds with known phase transitions at high temperatures have been clearly detected as pseudosymmetric with differences between the transformed and the original structures lower than 1.0 \AA{}. About 20 additional structures were detected with pseudosymmetric features under the same threshold. These compounds are considered as having a high probability of exhibiting a phase transition at higher temperatures. \textcopyright{} 1996 The American Physical Society.

New ferroelectric inorganic materials predicted in point group 4mm

The Inorganic Crystal Structure Database containing a total of 209 entries for 128 different materials reported in point group 4 mm, of which eight are for previously known ferroelectrics. Analysis of the remaining entries, assuming the structure determinations reported are correct, leads to the prediction of an additional 43 new ferroelectric materials. 15 were determined in space group P4mm, 11 in P4bm, one in P42 nm, one in P4cc, two in P42 mc, one in P42 bc, seven in I4mm, two in I4cm, one in I41 md and two in I41 cd. Numerous other structures are shown to have been assigned, most likely, to an incorrect space group. All but one of the materials reported in space group P4bm are predicted to be ferroelectric. New ferroelectrics predicted in point group 4 mm include K2[Pt(CN)4]Br0.3.3H2O, Nd0.33TaO3, YBaCuFeO5+δ, Ba2(TiO)(Si2O7), K2(NbO)2(SiO3)4, Ba6CoNb9O30, Sr2SbMnO6, Hg2AlF5.(H2O)2, Rb5Nb3OF18 and SrNi2(VO4)2.

Prediction of ferroelectricity in recent Inorganic Crystal Structure Database entries under space group Pba2

Three new entries in space group Pba2 in the 1995 edition of the Inorganic Crystal Structure Database have been examined in the light of previously developed criteria for the prediction of ferroelectricity. The structural prediction [Abrahams (1989). Acta Cryst. B45, 228–232] that seven of the 21 entries presented under this space group in the 1988 edition most likely corresponded to previously unrecognized ferroelectric materials is thereby updated. The atomic coordinates of [(NH2)2C(NHNH3)]ZrF6, among the new entries, are shown to satisfy the structural criteria; the maximum displacement along the polar axis required of any atom to undergo spontaneous polarization reversal is no larger than ~ 0.9 Å for a C or N atom and ~ 1.4 Å for a H atom, within the aminoguanidinium (2+) cation. By contrast, all atoms in the two independent ZrF6 anions are within 0.1 Å of an arrangement with zero spontaneous polarization. The characteristic force constant of the organic group is presently unknown, hence the Curie temperature for the crystal cannot be estimated. In the second new entry, the only atoms in the structure of the superconductor Ba0.6K0.4BiO23 at 403 K which depart significantly from a centrosymmetric arrangement are three of the four independent O atoms, one of which is at a site only 6% occupied. If these displacements are not artefacts, then this material is ferroelectric with an estimated Curie temperature in the range 410–740 K; a subsequent study, however, reported the structure in space group Pbam. The atomic coordinates of the final 1995 entry, (Cl3PNPCl3)(MoOCl4), do not differ significantly from centrosymmetry, in which case the material is not ferroelectic, apart from unequal occupancy of the Mo-atom sites. If the disorder model is correct and the two Mo sites are unequally occupied, then these sites cannot become equivalent and (Cl3PNPCl3)(MoOCl4) must remain polar without the possibility of becoming ferroelectric.

Inorganic crystal structure database (ICSD) and standardized data and crystal chemical characterization of inorganic structure types (TYPIX) - Two tools for inorganic chemists

The two databases ICSD and TYPIX are described. ICSD is a comprehensive compilation of crystal structure data of inorganic compounds (about 39 000 entries). TYPIX contains 3600 critically evaluated data sets representative of structure types formed by inorganic compounds.

Data Import and Validation in the Inorganic Crystal Structure Database.

In the following paper the input procedures for the Inorganic Crystal Structure Database (ICSD) will be outlined. The input flow of the data is explained. Since the data have been excerpted from journal articles a bibliometric analysis of the relevant literature is presented. The types of data and the form in which they are recorded are discussed. Finally, illustrations are given of the importance of data checking and the data checking procedures are described in detail.

Structure Correlation Methods in Chemical Crystallography

Abstract The structural information collected by X-ray (or neutron) diffraction studies of metallic, ionic, molecular and macromolecular crystals has increased beyond any previously imagined limit. Data are presently compiled in computer-based crystal structure databases. Making particular reference to molecular crystals, it is shown that the information collected may possess a great heuristic value, that is a great potential for guiding the discovery of new chemical facts or the formulation of new chemical theories, provided systematic methods of database analysis and crystal structure interpretation are made available. It is suggested that such methods consist of systematic correlations of structural data pertaining to single molecular fragments as found in many different crystal structures and can be collectively called (crystal) structure correlation methods (SCMs). SCMs are based on the search for and recognition of correlations among the geometrical descriptors of the fragment (structural correlatio...

A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding.

We propose a general mean field model of ligand-protein interactions to determine the thermodynamic equilibrium of a system at finite temperature. The method is employed in structural assessments of two human immuno-deficiency virus type 1 protease complexes where the gross effects of protein flexibility are incorporated by utilizing a data base of crystal structures. Analysis of the energy spectra for these complexes has revealed that structural and thermo-dynamic aspects of molecular recognition can be rationalized on the basis of the extent of frustration in the binding energy landscape. In particular, the relationship between receptor-specific binding of these ligands to human immunodeficiency virus type 1 protease and a minimal frustration principle is analyzed.

Inorganic crystal structure database. Design and operational experience

The Inorganic Crystal Structure Database is a section of the Databank on the Properties of Materials for Electronics that was created at the Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. The database, which is supplied with constantly updated software, includes quantitative structural data and is designed for solving materials-technology problems. The database contains information on crystal structures of complex and ordinary oxides (including compounds with HTSC properties), chalcogenides, intermetallic compounds, inorganic complexes, etc. More than 20 scientific works on different topics were performed using the database.

Algorithms for protein structural motif recognition.

The identification of protein sequences that fold into certain known three-dimensional (3D) structures, or motifs, is evaluated through a probabilistic analysis of their one-dimensional (1D) sequences. We present a correlation method that runs in linear time and incorporates pairwise dependencies between amino acid residues at multiple distances to assess the conditional probability that a given residue is part of a given 3D structure. This method is generalized to multiple motifs, where a dynamic programming approach leads to an efficient algorithm that runs in linear time for practical problems. By this approach, we were able to distinguish (2-stranded) coiled-coil from non-coiled-coil domains and globins from nonglobins. When tested on the Brookhaven X-ray crystal structure database, the method does not produce any false-positive or false-negative predictions of coiled coils.

The effective shapes and sizes of Cu2+ and Mn3+ ions in oxides and fluorides

Abstract Structural data, retrieved from the Inorganic Crystal Structure Database, have been used to study the effective shape and sizes of six coordinated Cu2+ and Mn3+ ions in oxides and fluorides. The distortions of the coordination octahedra for these two metal ions, essentially due to the structural implications of the Jahn-Teller effect, are assumed to be interpretable in terms of a nonspherical (ellipsoidal) effective shape of the metal ions. For octahedra with approximate tetragonal D 4h symmetry (rotational ellipsoid) a reasonable one-parameter correlation function is shown to be 2/r 4 2 + 1/r 2 2 = 3/r 0 2, where r 4 is the ionic size perpendicular to and r 2 the size along the rotation axis. The single parameter r 0 to be determined, estimated to 0.66(1) Å for Cu2+ and 0.59(1) Å for Mn3+, represents the size of the spherical case. From the correlation function, possible estimates of the effective sizes for square planar four coordination (and linear two coordination) can be obtained by extrapolation, giving 0.54 Å and 0.48 Å for four coordinated Cu2+ and Mn3+, respectively. According to the correlation function the radii decrease with the square root of the coordination number. For ions with effective ellipsoidal shapes like Cu2+ and Mn3+, it is shown that i.a. not only the use of average bond distances but also the previously used linear relation between average distances and distortion-parameters are strongly dependent on the degree of non-sphericity. A modified linear relation, between average bond distance and distortion, with improved linear correlation is suggested. As an alternative, the root harmonic mean square (rhms) value, 1/[unk], that gives an estimate of the parameter r 0, is suggested to be used for judging the relevance of an observed bond length distribution (R 1,…,R 6 and ri estimated Ri – r ligand) for six-coordinated ions.

Crystallographic and PM3-COSMO SCF-MO study of the structure and properties of aryloxy- or arylthio-thiazinones

The solid state structures of three para-substituted aryloxy- or arylthio-thiazinone derivatives reveal that the conformation of 2 differs from 1 and 3 in the orientation of the Y–aryl bond, due in part to an unusually strong CO ⋯ H–C–S intermolecular interaction of rO ⋯ H 2.20 A present in 2. A search of the Cambridge crystal structure database revealed relatively few other structures with similarly strong O ⋯ H–C interactions in which the common feature is the H–C–S structural unit. The observed reaction rate for aqueous hydrolysis of this series of compounds via attack of water at the C(2) position was found to correlate with the energy of the highest unoccupied orbital corresponding to σ rather than π character, but no feature in the wavefunctions could be found which identified 2 as the most likely to form the strongest O ⋯ H–C–S hydrogen bonding interaction in this series.

New developments for the Inorganic Crystal Structure Database (CSD)

New developments for the Inorganic Crystal Structure Database (CSD)

Quantum diagrams and the prediction of new materials

A statistically based diagrammatic scheme for classifying the full database of crystal structures of binary, ternary and quaternary compounds and the tendency to compound formation in binary and ternary alloy systems is used as the basis for the study of small sets of compounds of special interest. Diagrammatic regularities are observed in stable quasi-crystals, high T c ferroelectrics and high T c superconductors, reflecting a correlation of these types of order with local structure and stability. Detailed application to quasi-crystals uses these diagrammatic regularities to facilitate the recognition of phenomenological trends and to identify chemical factors which favor quasi-crystal formation. This provides severe constraints on compositions at which quasi-crystals or crystalline approximants are likely to form. Several computerized search strategies which utilize the diagrammatic conditions to identify compositions for experimental investigation are outlined.

Quantum diagrams, structural models and the prediction of new quasicrystals

A statistically-based diagrammatic scheme for classifying the full data base of crystal structures of binary, ternary and quaternary compounds and tendency to compound formation in binary and ternary alloy systems is used as the basis for the study of small sets of compounds of special interest. Application to quasicrystals results in the identification of diagrammatic regularities which facilitate the recognition of phenomenological trends and the identification of chemical factors which favor quasicrystal formation. This provides severe constraints on compositions at which quasicrystals or crystalline approximants are likely to form. A structural model is presented from which an additional quasicrystal condition is derived. Results of a computerized search which utilizes these conditions to identify compositions for experimental investigation are given.

Differences in the amino acid distributions of 3(10)-helices and alpha-helices.

Local determinants of 3(10)-helix stabilization have been ascertained from the analysis of the crystal structure data base. We have clustered all 5-length substructures from 51 nonhomologous proteins into classes based on the conformational similarity of their backbone dihedral angles. Several clusters, derived from 3(10)-helices and multiple-turn conformations, had strong amino acid sequence patterns not evident among alpha-helices. Aspartate occurred over twice as frequently in the N-cap position of 3(10)-helices as in the N-cap position of alpha-helices. Unlike alpha-helices, 3(10)-helices had few C-termini ending in a left-handed alpha conformation; most 3(10) C-caps adopted an extended conformation. Differences in the distribution of hydrophobic residues among 3(10)- and alpha-helices were also apparent, producing amphipathic 3(10)-helices. Local interactions that stabilize 3(10)-helices can be inferred both from the strong amino acid preferences found for these short helices, as well as from the existence of substructures in which tertiary interactions replace consensus local interactions. Because the folding and unfolding of alpha-helices have been postulated to proceed through reverse-turn and 3(10)-helix intermediates, sequence differences between 3(10)- and alpha-helices can also lend insight into factors influencing alpha-helix initiation and propagation.