Crystal Structure Database Research Articles

Global multinary structural chemistry of stable quasicrystals, high-TC ferroelectrics, and high-Tc superconductors.

A common feature of stable quasicrystals, high-${\mathit{T}}_{\mathit{C}}$ ferroelectrics, and high-${\mathit{T}}_{\mathit{c}}$ superconductors is that their unusual physical properties are correlated with characteristic crystal stuctures that are often vicinal to structural instabilities. We describe a statistically based diagrammatic scheme, due to Villars, for classifying the full database of crystal structures of binary, ternary, and quaternary compounds and tendency to compound formation in binary- and ternary-alloy systems. Principles of an expert system using this global organization to study small sets of compounds of special interest are formulated. Application to quasicrystals, ferroelectrics, and superconductors results in the identification of diagrammatic regularities which enable us to recognize phenomenological trends and to develop computerized search strategies for the prediction of new materials.

Analysis of side‐chain conformational distributions in neutrophil peptide‐5 nmr structures

The side-chain conformations have been analyzed in the antimicrobial peptide, Neutrophil Peptide-5 (NP-5), whose structure was independently generated from nmr-derived distance constraints using a distance geometry algorithm. The side-chain and peptide dihedral angle distributions in the nmr structures were compared with those constructed from a data base of high-resolution protein crystal structures. The side-chain conformational preferences for NP-5 in solution are significantly different from those observed in the crystal structure data base. These results indicate that the side-chain conformations are quite disordered for many of the residues of NP-5. The absence of a correlation between the width of the conformational distribution and surface accessibility suggests that the disorder may be due to limitations in the structural information extracted from the nmr data rather than to molecular motion. However, it is also observed that the degree of conformational disorder is only weakly correlated with the number of nuclear Overhauser enhancements to a given side chain. Possible reasons for this are discussed. Molecular mechanics refinement of these structures did not significantly change the side-chain populations. Anomolously wide distributions are observed for rotations about the peptide bonds and the disulfide bonds in the NP-5 distance geometry structures, which are improved by the refinement. The very high degree of order observed for the central dihedral angle of the disulfide bond in the high-resolution crystal data base suggests that the rotation about this bond in proteins is determined by the local potential.

Systematic prediction of new ferroelectrics on the basis of structure

Abstract An inorganic pyroelectric crystal is predicted to be ferroelectric if it satisfies the structural conditions that no atom within the unit cell be displaced more than about 1 Å from the position it would occupy in the paraelectric state and that the largest such displacement be greater than about 0.1 Å. In addition, the phase transition temperature, as estimated from the AKJ proportionality to the square of the largest critical atomic displacement [Phys. Rev. 172, 551 (1968)], should not exceed about 2000 K. These conditions have been used as successful predictors of ferroelectricity in SrAlF5 and in Pb3(MF6)2 with M = Ti, V, Cr, Fe and Ga. The recent availability of the Inorganic Crystal Structure Database, with its current 2943 entries in polar space groups, offers the possibility of applying these predictors systematically to all structurally determined inorganic pyroelectrics. Eleven of the total 68 polar space groups have now been examined, resulting in the prediction of over 50 new ferroelectric crystals.

ChemInform Abstract: Using Chemical Bonds to Analyze Data Retrieved from the Inorganic Crystal Structure Database.

The programs SINDBAD (batch) and STRUMO (interactive) use a chemical bond model to examine structures retrieved from the Inorganic Crystal Structure Database. The bonding topology at any desired level of bond strength is determined from the bonds (and their valences) calculated directly from the atomic coordinates stored in the database. Hydrogen bonding, disorder, internal stress, defects, and diffusion paths can be examined and modeled by using related techniques

Predicting surface exposure of amino acids from protein sequence

The amino acid residues on a protein surface play a key role in interaction with other molecules, determined many physical properties, and constrain the structure of the folded protein. A database of monomeric protein crystal structures was used to teach computer-simulated neural networks rules for predicting surface exposure from local sequence. These trained networks are able to correctly predict surface exposure for 72% of residues in a testing set using a binary model, (buried/exposed) and for 54% of residues using a ternary model (buried/intermediate/exposed). In the ternary model, only 11% of the exposed residues are predicted as buried and only 5% of the buried residues are predicted as exposed. Also, since the networks are able to predict exposure with a quantitative confidence estimate, it is possible to assign exposure for over half of the residues in a binary model with greater than 80% accuracy. Even more accurate predictions are obtained by making a consensus prediction of exposure for a homologous family. The effect of the local environment of an amino acid on its accessibility, though smaller than expected, is significant and accounts for the higher success rate of prediction than obtained with previously used criteria. In the absence of a three-dimensional structure, the ability to predict surface accessibility of amino acids directly from the sequence is a valuable tool in choosing sites of chemical modification or specific mutations and in studies of molecular interaction.

薬物分子設計における結晶構造データベースの活用

薬物分子設計における結晶構造データベースの活用

The conformational effects of quaternary centres

Quaternary centres impose a particularly simple conformational regime on adjacent acyclic bonds; this is shown by force field calculations on alkanes and confirmed by crystal structure database studies on quaternary ammonium ions; possible implications are considered.

Structurally based predictions of ferroelectricity in seven inorganic materials with space group Pba2 and two experimental confirmations

Application of structural criteria presented previously, to all entries in the Inorganic Crystal Structure Database for materials crystallizing in space group Pba2, has led to the prediction of seven new ferroelectrics. These materials, with estimates of their respective predicted transition temperatures (To) to an assumed paraelectric phase, are: Na~3Nb35094 (340 K), K3FesF15 (535K), Mo17047 (1750K), Bi3NblTO47 (500 K), Ba~sPr38TiT202~ 6 (650K), K3Sb50~4 (340K) and CaEGeTO~6 (close to room temperature if the structure determination is correct). Experimental confirmation has now been made for two of these predictions, with a T c of 320 (10)K found in Na13Nb35094 and 490 (10) K found in K3Fe5F~5. Five of the newly predicted ferroelectrics are related to the tetragonal-bronze structure.

What factors determine cation coordination numbers?

Over 14 000 coordination environments of 100 different cations retrieved from the Inorganic Crystal Structure Database have been analyzed. For comparison predicted coordination numbers (PCN's) have been calculated using ionic radius ratios. The observed coordination numbers are generally smaller than or equal to the PCN's and their range, for most cations, can be predicted from a knowledge of the Lewis-base strengths of available anions and the requirement that these strengths be close to the Lewis-acid strength of the cation. The occurrence of smaller coordination numbers is associated with strongly directed bonds (electronic effects) and is found for main-group elements in low oxidation states and for closed-d-shell cations of Groups 11, 12 and 13. An analysis of the results shows that to use ionic radii to predict both coordination numbers and interatomic distances it is necessary to use cation and anion radii that both vary in the same way with the cation coordination number (N). The value found for the oxygen radius is 1.12 + 0.23In(N-2)/~. The average observed coordination number is used to calculate cation Lewis-acid strengths which are shown to correlate with electronegativity.

Crystallographic modelling.

The project on crystallographic modelling aims at extending the application of interactive graphics to inorganic structures. Starting from the available expertise in organic and protein modelling, the symmetry of the crystal structure is used not only to draw fixed models of many unit cells of the structure, which as an entity can be interactively manipulated, but also to change details of the structures interactively with retention of the original symmetry. Real-time shifts of atom positions are automatically applied to all symmetry-equivalent atoms given the symmetry constraints. This also applies to translations and rotations of groups of atoms. In order to get feedback about these structural changes one can simulate powder diffraction patterns in real-time mode and compare them with the experimental powder patterns. These features are crucial in truly crystallographic modelling, but have not been implemented before in other programs. The program can be used in combination with standard molecular modelling programs and is also interfaced to the Inorganic Crystal Structure Database. Before describing the realization of these features on state-of-the-art hardware, we will review the expertise in molecular modelling and discuss an MS-DOS program to study inorganic crystal structures.

A statistical analysis of magic numbers of valence electrons in small clusters of transition metals using the Cambridge Crystal Structure Database

Distribution of small clusters of transition metals M n with n = 3 to 6 metal atoms over the number of valence electrons in metallopolyhedra, N val, has been analysed using the Cambridge Crystal Structure Database (10 sets, total 923 crystal structures). The occurrence of peaks related to magic numbers N val has been found for trinuclear (48e), tetranuclear (60e) and hexanuclear (86e) carbonyl clusters of metals of the Fe and Co subgroups. However, similar distributions for pentanuclear carbonyl clusters of the same metals, for tri- and tetranuclear carbonyl-phosphine derivatives of metals of the Ni subgroup, and also for the M 4(μ 3-X) 4 type clusters with mixed cubane-like frameworks (where X is a halogen or chalcogen) are more uniform and exhibit no predominance of specific “magic” numbers. Among tri- and tetranuclear metal complexes of the Cu subgroup, the more common and typical are those with no metal-metal bonds, in which every metal atom has a 17-, 18-, or 19-electron valence shell. On going from metals of the Fe and Co subgroups to post-transition elements, the strength of metal-metal bonds and the descriptive ability of magic numbers decline. The following magic numbers were found for octahedral “inorganic” clusters of early transition metals: N val = 74 for clusters of the M 6(μ 3-X) 12 type (where X is a halogen) and a more strictly obeyed number N val=84 valid for more rigid frameworks M 6(μ 3-X) 8, (X is halogen or chalcogen).

A real-space computer-based symmetry algebra

A computer-based symmetry algebra is described which permits the reconstruction of an infinite bond network from the asymmetric connectivity without an a priori knowledge of atomic coordinates. The algebra requires not only an algorithmic ordering of the Wyckoff groups but the designation of one site in each Wyckoff group as a special-position representative (SPR) site. The algebra is designed to be used for analysing the bonding network of compounds appearing in the Inorganic Crystal Structure Database.

Data base for inorganic crystal structures

Crystal structure data base form a typical example for the advantages of numerical data bases. They store the long row of Primary results in such a manner that they can be checked and evaluated by computer programs. Thus giving results of structural work in an appropriate presentation to all need them.

結晶構造データベースのサービスの現状

結晶構造データベースのサービスの現状

The inorganic crystal structure data base

An inorganic crystal structure data base is described which will, when completed in the next year, contain details of all the 23 OOO published structum of inorganic crystals. This pper describes the structure of the data base, the procedures used to check the data as they are entered, and the program used to access them. Plans for the future development of the data base system include defining search keys on the basis of bonding topologies and crystal structure types as well as plans for providing an integrated crystal structure retrieval system.