Showing papers in "Acta Crystallographica Section B-structural Science in 2002"

The Cambridge Structural Database: a quarter of a million crystal structures and rising

Abstract: The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500000 crystal structures by the year 2010.

New software for searching the Cambridge Structural Database and visualizing crystal structures

Abstract: Two new programs have been developed for searching the Cambridge Structural Database (CSD) and visualizing database entries: ConQuest and Mercury The former is a new search interface to the CSD, the latter is a high-performance crystal-structure visualizer with extensive facilities for exploring networks of intermolecular contacts Particular emphasis has been placed on making the programs as intuitive as possible Both ConQuest and Mercury run under Windows and various types of Unix, including Linux

New developments in the Inorganic Crystal Structure Database (ICSD): accessibility in support of materials research and design.

Abstract: The materials community in both science and industry use crystallographic data models on a daily basis to visualize, explain and predict the behavior of chemicals and materials. Access to reliable information on the structure of crystalline materials helps researchers concentrate experimental work in directions that optimize the discovery process. The Inorganic Crystal Structure Database (ICSD) is a comprehensive collection of more than 60 000 crystal structure entries for inorganic materials and is produced cooperatively by Fachinformationszentrum Karlsruhe (FIZ), Germany, and the US National Institute of Standards and Technology (NIST). The ICSD is disseminated in computerized formats with scientific software tools to exploit the content of the database. Features of a new Windows-based graphical user interface for the ICSD are outlined, together with directions for future development in support of materials research and design.

Investigation of the structure and phase transitions in the novel A-site substituted distorted perovskite compound Na0.5Bi0.5TiO3

Abstract: Rietveld neutron powder profile analysis of the compound Na0.5Bi0.5TiO3 (NBT) is reported over the temperature range 5–873 K. The sequence of phase transitions from the high-temperature prototypic cubic structure (above 813 K), to one of tetragonal (673–773 K) and then rhombohedral structures (5–528 K) has been established. Coexisting tetragonal/cubic (773–813 K) and rhombohedral/tetragonal (with an upper temperature limit of 145 K between 528 and 673 K) phases have also been observed. Refinements have revealed that the rhombohedral phase, space group R3c, with aH = 5.4887 (2), cH = 13.5048 (8) A, V = 352.33 (3) A3, Z = 6 and Dx = 5.99 Mg m−3, exhibits an antiphase, a−a−a− oxygen tilt system, ω = 8.24 (4)°, with parallel cation displacements at room temperature. The tetragonal phase, space group P4bm, with aT = 5.5179 (2), cT = 3.9073 (2) A, V = 118.96 (1) A3, Z = 2 and Dx = 5.91 Mg m−3, possesses an unusual combination of in-phase, a0a0c+ oxygen octahedra tilts, ω = 3.06 (2)°, and antiparallel cation displacements along the polar axis. General trends of cation displacements and the various deviations of the octahedral network from the prototypic cubic perovskite structure have been established and their systematic behaviour with temperature is reported. An investigation of phase transition behaviour using second harmonic generation (SHG) to establish the centrosymmetric or non-centrosymmetric nature of the various phases is also reported.

Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

Abstract: The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

The structure of trititanate nanotubes

Abstract: A comprehensive chemical and structural analysis is made of a new type of trititanate nanotube, which is synthesized via the reaction of TiO2 particles with NaOH aqueous solution. It is found that the trititanate nanotubes are multi-walled scroll nanotubes with an inter-shell spacing of about 0.78 nm and an average diameter of about 9 nm. An atomic model of the nanotube is derived based on information from powder X-ray diffraction, selective-area electron diffraction, high-resolution electron microscopy and structure simulations. A model nanotube may be constructed by wrapping a (100) sheet of H2Ti3O7 along [001] with the tube axis parallel to [010].

Crystal structure prediction of small organic molecules: a second blind test

Abstract: The first collaborative workshop on crystal structure prediction (CSP1999) has been followed by a second workshop (CSP2001) held at the Cambridge Crystallographic Data Centre. The 17 participants were given only the chemical diagram for three organic molecules and were invited to test their prediction programs within a range of named common space groups. Several different computer programs were used, using the methodology wherein a molecular model is used to construct theoretical crystal structures in given space groups, and prediction is usually based on the minimum calculated lattice energy. A maximum of three predictions were allowed per molecule. The results showed two correct predictions for the first molecule, four for the second molecule and none for the third molecule (which had torsional flexibility). The correct structure was often present in the sorted low-energy lists from the participants but at a ranking position greater than three. The use of non-indexed powder diffraction data was investigated in a secondary test, after completion of the ab initio submissions. Although no one method can be said to be completely reliable, this workshop gives an objective measure of the success and failure of current methodologies.

Group-theoretical analysis of octahedral tilting in ferroelectric perovskites.

Abstract: Group-theoretical methods are used to analyze perovskite structures where both ferroelectric cation displacements and simple tilting of octahedral units are present. This results in a list of 40 different structures, each with a unique space-group symmetry. The list is compared with that of Aleksandrov & Bartolome [Phase Transit. (2001), 74, 255–335] and a number of differences are found. The group–subgroup relationships between the structures are also determined, along with an indication of those phase transitions that must be first order by Landau theory.

The Nucleic Acid Database

Abstract: The Nucleic Acid Database was established in 1991 as a resource to assemble and distribute structural information about nucleic acids. Over the years, the NDB has developed generalized software for processing, archiving, querying and distributing structural data for nucleic acid-containing structures. The architecture and capabilities of the Nucleic Acid Database, as well as some of the research enabled by this resource, are presented in this article.

Fast estimation of crystal densities

Abstract: A simple, efficient and accurate method for the estimation of crystal densities is of interest for different applications. By analysis of the Cambridge Structural Database (CSD) we derived an average atom volume method to estimate the cell volume for a given formula and Z value. This method extends the work of Mighell et al. (1987) by inclusion of the thermal expansion and error estimation.

The formation of paracetamol (acetaminophen) adducts with hydrogen-bond acceptors

Abstract: The crystal structures of five hemiadducts of paracetamol with 1,4-dioxane, N-methylmorpholine, morpholine, N,N-dimethylpiperazine and piperazine and a related 1:1 adduct of paracetamol with 4,4′-bipyridine are described. All structures are characterized by the formation of chains of paracetamol molecules, which are linked via either OH⋯O=C interactions [C(9) chains in graph-set notation] or NH⋯O=C interactions [C(4) chains], depending on the presence or absence of substituent groups on the guest molecule. In all cases except for the morpholine and bipyridine adducts these chains are connected by hydrogen-bond interactions with the guest molecules, which reside on crystallographic inversion centres. In the bipyridine adduct this linkage also involves a π-stacking interaction; in the morpholine adduct it is formed between the OH groups of two opposed paracetamol molecules. Most adducts (that with 4,4′-bipyridine is an exception) decompose on heating to give monoclinic paracetamol. This is the first systematic study of a series of co-crystals containing paracetamol.

Some 60 new space-group corrections

Abstract: Some 60 examples of crystal structures are presented which can be better described in space groups of higher symmetry than used in the original publications. These are divided into three categories: (A) incorrect Laue group (33 examples), (B) omission of a center of symmetry (22 examples), (C) omission of a center of symmetry coupled with a failure to recognize systematic absences (nine examples). Category A errors do not lead to significant errors in molecular geometry, but these do accompany the two other types of error. There are 19 of the current set of examples which have publication dates of 1996 or later. Critical scrutiny on the part of authors, editors and referees is needed to eliminate such errors in order not to impair the role of crystal structure analysis as the chemical court of last resort.

The Powder Diffraction File: present and future.

Abstract: The International Centre for Diffraction Data (ICDD) produces the Powder Diffraction File (PDF). This paper discusses some of the seminal events in the history of producing this primary reference for powder diffraction. Recent key events that center on collaborative initiatives have led to an enormous jump in entry population for the PDF. Collective efforts to editorialize the PDF are ongoing and provide enormous added value to the file. Recently, the ICDD has created a new series of the PDF, designated PDF-4. These relational database structures are being used to house the PDF of the future. The design and benefits of the PDF-4 are described.

Structural relationships between cations and alloys; an equivalence between oxidation and pressure.

Abstract: More than 100 examples are provided of the structural identity between the cation arrays in oxides and their corresponding alloys (binary compounds). Halides and halogenates, sulfides and sulfites and/or sulfates, selenides and selenates, phosphides and phosphates show this behaviour. In some cases, the structure of the cation subarray corresponds to the structure of the alloy at ambient conditions, but in other cases, cations stabilize structures which correspond to those of the high-pressure phases of the alloy, from which an analogy between the insertion of oxygen and the application of pressure can be established. In this last case, the oxides show polymorphism with temperature and when heated, the structure of the ambient pressure of the alloy is recovered as if heating would compensate the effect of pressure. From the results reported here, it is concluded that cations do not seem to be either the isolated entities, predicted by the ionic model, which occupy interstices of an oxygen matrix, or they arrange in a more or less arbitrary way, but they try to reproduce the structure of their corresponding alloy. Many of the phase transitions and the polymorphism exhibited by the oxides described here are better explained when they are considered as formed by previous entities which are the alloys. Oxides should be considered as `real stuffed alloys'. These features do not seem to be casual, but they obey a general principle: Cations recognize themselves in spite of being embedded in an oxygen bulk. The nature and the physical meaning of this recognition are problems which remain unsolved.

CIF: the computer language of crystallography

Abstract: The Crystallographic Information File (CIF) was adopted in 1990 by the International Union of Crystallography as a file structure for the archiving and distribution of crystallographic information. The CIF standard is now well established and is in regular use for reporting crystal structure determinations to Acta Crystallographica and other journals. The structure of CIF is flexible and extensible and is compatible with other evolving standards. It is well suited to relational and object-oriented models, and is being adopted by the crystallographic databases. This paper reviews the development of CIF and describes its salient features. Future extension of the standard to include implementation of methods will allow CIF to exploit the potential of advanced information-handling software.

Crystal chemistry of zirconosilicates and their analogs: topological classification of MT frameworks and suprapolyhedral invariants.

Abstract: The first attempt is undertaken to consider systematically topological structures of zirconosilicates and their analogs (60 minerals and 34 synthetic phases), where the simplest structure units are MO6 octahedra and TO4 tetrahedra united by vertices ([TO4]:[MO6] = 1:1–6:1). A method of analysis and classification of mixed three-dimensional MT frameworks by topological types with coordination sequences {Nk} is developed, which is based on the representation of crystal structure as a finite `reduced' graph. The method is optimized for the frameworks of any composition and complexity and implemented within the TOPOS3.2 program package. A procedure of hierarchical analysis of MT-framework structure organization is proposed, which is based on the concept of polyhedral microensemble (PME) being a geometrical interpretation of coordination sequences of M and T nodes. All 12 theoretically possible PMEs of MT6 polyhedral composition are considered where T is a separate and/or connected tetrahedron. Using this methodology the MT frameworks in crystal structures of zirconosilicates and their analogs were analyzed within the first 12 coordination spheres of M and T nodes and related to 41 topological types. The structural correlations were revealed between rosenbuschite, lavenite, hiortdahlite, woehlerite, siedozerite and the minerals of the eudialyte family.

Applications of the Cambridge Structural Database to molecular inorganic chemistry

Abstract: Applications of the data in the Cambridge Structural Database (CSD) to knowledge acquisition and fundamental research in molecular inorganic chemistry are reviewed. Various classes of application are identified, including the derivation of typical molecular dimensions and their variability and transferability, the derivation and testing of theories of molecular structure and bonding, the identification of reaction paths and related conformational analyses based on the structure correlation hypothesis, and the identification of common and presumably energetically favourable intermolecular interactions. In many of these areas, the availability of plentiful structural data from the CSD is set against the emergence of high-quality computational data on the geometry and energy of inorganic complexes.

Structure solution of the basic decagonal Al-Co-Ni phase by the atomic surfaces modelling method.

Abstract: The atomic surfaces modelling technique has been used to solve the structure of the basic Ni-rich Al–Co–Ni decagonal phase. Formula Al70.6Co6.7Ni22.7, space group P\overline{10}, five-dimensional unit-cell parameters: d1 = d4 = 4.752 (3) A, d2 = d3 = 3.360 (2) A, d5 = 8.1710 (2) A; α12 = α34 = 69.295°, α13 = α24 = 45°, α14 = 41.410°, α23 = αi5 = 90° (i = 1–4), V = 291.2 (7) A5; Dx = 3.887 Mg m−3. Refinement based on |F|; 2767 unique reflections (|F| > 0), 749 parameters, R = 0.17, wR = 0.06. Describing the structure of quasicrystals embedded in n-dimensional superspace in principle takes advantage of n-dimensional periodicity to select the minimal set of degrees of freedom for the structure. The method of modelling of the atomic surfaces yielded the first fully detailed structure solution of this phase. Comparison with numerous former, less accurate models confirms several features already derived, but adds a new essential insight of the structure and its complexity. The atoms fill the space forming recurrent structure motifs, which we will (generically) refer to as clusters. However, no unique cluster exists, although differences are small. Each cluster shows a high degree of structural disorder. This gives rise to a large configurational entropy, as much as expected in a phase which is stable at high temperature. On the other side, the cluster spatial arrangement is perfectly quasiperiodic. These considerations, corroborated by analysis of the structural relationship with neighbouring periodic phases, strongly suggest the existence of a non-local, long-range interaction term in the total energy which may be essential to the stability.

CRYSTMET: a database of the structures and powder patterns of metals and intermetallics.

Abstract: CRYSTMET is a database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) and associated bibliographic, chemical and physical information. Also included are simulated powder diffraction patterns for all of the entries. The database currently contains almost 70000 entries and covers the literature exhaustively from 1922 to the present. The database is available on CD-ROM with search/analysis software for use on personal computers. This software can be used with any database in the appropriate format; currently CRYSTMET and the ICSD databases are available. This paper describes the database content, the procedures used in its construction, the software made available to the user and a number of potential uses for the data.

Structural characterization of crystals of α-glycine during anomalous electrical behaviour

Abstract: The crystal structure of α-glycine has been investigated in the temperature range 288–427 K using neutron diffraction. The molecular structure does not change significantly and the putative crystallographic phase transition associated with anomalous electrical behaviour in this temperature range is not observed. The unit cell expands anisotropically with increasing temperature, with the unique monoclinic b axis, corresponding to the stacking direction of molecular layers, changing the most. The increasing separation of antiferroelectric molecular layers with increasing temperature is driven by an increase in molecular libration about an axis that lies perpendicular to the b axis. There is also a weakening of the interlayer hydrogen bonds with temperature. These structural and dynamic changes will affect the response of molecular dipoles to an applied electric field and provide a possible mechanism for the anomalous electrical behaviour.

An exceptionally stable peptide nanotube system with flexible pores.

Abstract: The hydrophobic channels in the structure of the dipeptide l-alanyl-l-valine act as supramolecular hosts for organic solvent molecules. In a series of data collections, it is demonstrated that small molecules like acetonitrile, methanol and acetone can be removed from the channels by drying without impairing the structure of the hydrogen-bonded peptide host structure. The title compound is one of the very first organic molecules to be found to have this property. Alcohol guests larger than methanol are also absorbed, but they induce a doubling of two axes and a change in the shape and size of the pores. The observed structural modifications explain why these solvent molecules are more or less irreversibly trapped inside the channels.

The mapping of electronic energy distributions using experimental electron density.

Abstract: It is demonstrated that the approximate kinetic energy density calculated using the second-order gradient expansion with parameters of the multipole model fitted to experimental structure factors reproduces the main features of this quantity in a molecular or crystal position space. The use of the local virial theorem provides an appropriate derivation of approximate potential energy density and electronic energy density from the experimental (model) electron density and its derivatives. Consideration of these functions is not restricted by the critical points in the electron density and provides a comprehensive characterization of bonding in molecules and crystals.

New Powder Diffraction File (PDF-4) in relational database format: advantages and data-mining capabilities

Abstract: The International Centre for Diffraction Data (ICDD) is responding to the changing needs in powder diffraction and materials analysis by developing the Powder Diffraction File (PDF) in a very flexible relational database (RDB) format. The PDF now contains 136 895 powder diffraction patterns. In this paper, an attempt is made to give an overview of the PDF-4, search/match methods and the advantages of having the PDF-4 in RDB format. Some case studies have been carried out to search for crystallization trends, properties, frequencies of space groups and prototype structures. These studies give a good understanding of the basic structural aspects of classes of compounds present in the database. The present paper also reports data-mining techniques and demonstrates the power of a relational database over the traditional (flat-file) database structures.

Symmetrieverwandtschaften bei Varianten des Perowskit-Typs

Abstract: The relationships among the huge number of derivative structures of the perovskite type are rationalized in a concise manner using group–subgroup relations between space groups One family tree of such relations is given for perovskites having tilted coordination octahedra Further group–subgroup relations are concerned with distortions of the octahedra, such as Jahn–Teller distortions or with atoms shifted from the octahedron centres In these cases, the space-group symmetry reductions must allow site symmetry reductions of the occupied sites in the perovskite structure On the other hand, subgroups in which the perovskite sites split into different independent sites are necessary for derivative structures with atom substitutions, such as in the elpasolites A2EMX6 In addition, substitutions and distortions can be combined in adequate subgroups Substitutions may also involve the occupation of atom sites of perovskite by molecular groups such as N(CH3)4+ or other organic cations, or by molecules like acetonitrile If they are ordered, their molecular symmetry requires further space-group symmetry reductions The anions can be replaced by cyanide ions or by NO2− ions; space-group symmetry then depends on the temperature-dependent degree of order The relationships can be used to predict if and what kind of twinning may occur in phase transitions and whether second-order phase transitions are possible

Life-science applications of the Cambridge Structural Database

Abstract: Several studies show that the molecular geometries and intermolecular interactions observed in small-molecule crystal structures are relevant to the modelling of in vivo situations, although the influence of crystal packing is sometimes important and should always be borne in mind. Torsional distributions derived from the Cambridge Structural Database (CSD) can be used to map out potential-energy surfaces and thereby help identify experimentally validated conformational minima of molecules with several rotatable bonds. The use of crystallographic data in this way is complementary to in vacuo theoretical calculations since it gives insights into conformational preferences in condensed-phase situations. Crystallographic data also underpin many molecular-fragment libraries and programs for generating three-dimensional models from two-dimensional chemical structures. The modelling of ligand binding to metalloenzymes is assisted by information in the CSD on preferred coordination numbers and geometries. CSD data on intermolecular interactions are useful in structure-based inhibitor design both in indicating how probable a protein-ligand interaction is and what its geometry is likely to be. They can also be used to guide searches for bioisosteric replacements. Crystallographically derived information has contributed to many life-science software applications, including programs for locating binding 'hot spots' on proteins, docking ligands into enzyme active sites, de novo ligand design, molecular superposition and three-dimensional QSAR. Overall, crystallographic data in general, and the CSD in particular, are very significant tools for the rational design of biologically active molecules.

Analyzing experimental electron density with the localized-orbital locator.

Abstract: The localized-orbital locator, which describes the features of bonding in terms of the local kinetic energy, is approximately expressed as a function of electron density and its first and second derivatives. Calculations based on accurate electron densities derived from X-ray diffraction data are carried out for crystals with different types of chemical bonds. It is demonstrated that the localized-orbital locator reveals the features of atomic interactions in a solid state and allows the covalent, ionic and van der Waals bonds to be distinguished.

CH3CN: X-ray structural investigation of a unique single crystal. β → α phase transition and crystal structure

Abstract: The phase transition from the low- (β) to the high-temperature (α) form of acetonitrile, CH3CN, has been directly observed and studied on a unique single crystal. Both the β and α structures have been determined at temperatures close to the transition temperature (206 K and 201 K), taking advantage of the hysteresis. A single crystal of the β form was obtained for the first time.

The self-hosting structure of β-Ta

Abstract: Using electrodeposition from a bath of molten fluorides, single crystals of tetragonal β-tantalum have been obtained for the first time at normal pressure. The unit-cell parameters are a = 10.211 (3), c = 5.3064 (10) A, space group P\bar 421m. The β-Ta structure belongs to the σ-type Frank–Kasper structures which are typical for binary intermetallic compounds and β-U. In comparison to the σ-type, additional intercalated Ta atoms (population factor ∼0.01) have been detected between the atoms located in the channels of the structure. The shorter interatomic distances observed between the channel atoms in comparison with the atoms of the framework justify the `self-hosting' characteristic. β-Ta exhibits common features with the complex tetragonal structures of the high-pressure phases for the elements Rb, Ba, Sr, Bi and Sb.

Terephthalate salts of dipositive cations.

Abstract: The crystal structures of M(C8H4O4)(H2O)2, M = Mg, Mn, Fe and Co, have been determined by applying Monte Carlo simulated annealing techniques to synchrotron powder diffraction data and refined by the Rietveld method using both synchrotron and laboratory powder data. These isostructural compounds crystallize in the monoclinic space group C2/c, with 18.2734 (9) ≤ a ≤ 18.7213 (13), 6.5186 (13) ≤ b ≤ 6.5960 (4), 7.2968 ≤ c ≤ 7.4034 (6) A, 98.653 (2) ≤ β ≤ 99.675 (1)° and Z = 4. The structure consists of alternating layers (perpendicular to a) of terephthalate anions and octahedrally coordinated metal cations. The octahedra are isolated; each carboxylate bridges two metal cations. The equatorial metal coordination consists of four terephthalate O atoms and there are two axial water molecules. Both water-molecule H atoms participate in normal-strength hydrogen bonds to carboxylate O atoms. Quantum chemical calculations (using CASTEP) were used to determine the H-atom positions and analyze the hydrogen bonding and the metal coordination. Both the atomic charges and the M—O bond-overlap populations indicate that, despite the fact that these compounds are isostructural, the metal–terephthalate bonding is different. The bonding in the Mg complex is essentially ionic, while the M—O bonds in the Mn, Fe and Co complexes have significant covalent character. Comparison of a new Rietveld refinement of the structure of copper(II) terephthalate trihydrate with the reported single-crystal structure provides an opportunity to assess the accuracy and precision that can be expected from structures of aromatic carboxylates determined using X-ray powder data. The average difference between the bond distances in the two structures is 0.03 A and the average difference in bond angles is only 1.1°.

Pressure-induced polymorphism in phenol

Abstract: The high-pressure crystal structure of phenol (C6H5OH), including the positions of the H atoms, has been determined using a combination of single-crystal X-ray diffraction techniques and ab initio density-functional calculations. It is found that at a pressure of 0.16 GPa, which is just sufficient to cause crystallization of a sample held at a temperature just above its ambient-pressure melting point (313 K), a previously unobserved monoclinic structure with P21 symmetry is formed. The structure is characterized by the formation of hydrogen-bonded molecular chains, and the molecules within each chain adopt a coplanar arrangement so that they are ordered in an alternating 1-1-1 sequence. Although the crystal structure of the ambient-pressure P1121 phase is also characterized by the formation of molecular chains, the molecules adopt an approximate threefold arrangement. A series of ab initio calculations indicates that the rearrangement of the molecules from helical to coplanar results in an energy difference of only 0.162 eV molecule−1 (15.6 kJ mole−1) at 0.16 GPa. The calculations also indicate that there is a slight increase in the dipole moment of the molecules, but, as the high-pressure phase has longer hydrogen-bond distances, it is found that, on average, the hydrogen bonds in the ambient-pressure phase are stronger.