Crystal Structure Database Research Articles

Novel Structural Parameters of Ig-Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity.

Antibody–antigen complexes challenge our understanding, as analyses to date failed to unveil the key determinants of binding affinity and interaction specificity. We partially fill this gap based on novel quantitative analyses using two standardized databases, the IMGT/3Dstructure-DB and the structure affinity benchmark. First, we introduce a statistical analysis of interfaces which enables the classification of ligand types (protein, peptide, and chemical; cross-validated classification error of 9.6%) and yield binding affinity predictions of unprecedented accuracy (median absolute error of 0.878 kcal/mol). Second, we exploit the contributions made by CDRs in terms of position at the interface and atomic packing properties to show that in general, VH CDR3 and VL CDR3 make dominant contributions to the binding affinity, a fact also shown to be consistent with the enthalpy–entropy compensation associated with preconfiguration of CDR3. Our work suggests that the affinity prediction problem could be partially solved from databases of high resolution crystal structures of complexes with known affinity.

Role of halogen substituents in a series of polymorphic 2,5-diamino-3,6-dicyanopyrazine derivatives with highly flexible groups

Abstract The crystal structures of the ortho-X-benzyl derivatives, where X=F, Cl, Br, I, and Me, of 2,5-bis(N,N-dibenzylamino)-3,6-dicyanopyrazine dyes (C34H24N6X4) were analysed to evaluate the effect of a systematic series of structures on the occurrence of polymorphism. Detailed crystal structure analysis indicated that the thermally stable forms of the polymorphic derivatives (Cl and Br derivatives) were close-packed, whereas those of the non-polymorphic derivatives (F and I derivatives) were stabilised by an intermolecular interaction involving the ortho-substituents. In the thermally metastable forms of the polymorphic derivative, halogen-halogen and halogen-nitrogen interactions contributed to the stabilisation of these crystals in the same way as the thermally stable form of the non-polymorphic derivatives. This indicated that the ease of polymorph occurrence would require an appropriate balance between the crystal energy of the close-packed structure and that of the crystal structure generated mainly by the electrostatic interactions involving the halogens in these halogenated pyrazine derivatives. In addition, the similar tendency of the occurrence of polymorphs in these halogenated pyrazine derivatives was found in 19 sets of halogenated compounds having known crystal structures of F, Cl, Br and I derivatives including at least one polymorphic derivative in the crystal structure database.

Antisoma Application: A Fully Integrated V-Like Antibodies Platform

Antibodies, also called immunoglobulins, are large Y-shaped proteins which are produced and used by the immune system in order to identify and neutralize foreign substances called antigens. The study and research of antibodies is a critical issue in science and has led in remarkable results with medical applications such as diseases diagnosis, therapies and antibodies related drugs. Due to the importance of antibodies, a comprehensive database of full length protein sequences or crystal structures of immunoglobulin (IG) and T cell receptor (TR) V-like protein sequences from human and other vertebrate species has been created. In this article, we study in detail the unique numbering system for immunoglobulins of IMGT, we correlate the database antibody entries and we provide a more in detailed approach into the data. Finally, due to the deviation of the expected from the real data, a user friendly application has been created. This powerful and flexible tool manipulates the antibodies V-like protein sequences with the approach described below and gives the opportunity to the user to extract and study the results and its physicochemical properties. The need for new therapeutic targets and the development of more potent drugs is enormous, despite the efforts and the investments all these years for the development of novel next generation drugs, the discovery and the characterization of new therapeutic targets using immunoglobulins or antibodies. The final outcome from this project will support the development of novel therapies. Antisoma can be freely downloaded from http://www.dimvl.com/antisoma.

Accelerating the exploration of Li/Na-ion battery materials via enlarged crystal structure databases

Accelerating the exploration of Li/Na-ion battery materials via enlarged crystal structure databases

The thermodynamic scale of inorganic crystalline metastability.

The space of metastable materials offers promising new design opportunities for next-generation technological materials, such as complex oxides, semiconductors, pharmaceuticals, steels, and beyond. Although metastable phases are ubiquitous in both nature and technology, only a heuristic understanding of their underlying thermodynamics exists. We report a large-scale data-mining study of the Materials Project, a high-throughput database of density functional theory-calculated energetics of Inorganic Crystal Structure Database structures, to explicitly quantify the thermodynamic scale of metastability for 29,902 observed inorganic crystalline phases. We reveal the influence of chemistry and composition on the accessible thermodynamic range of crystalline metastability for polymorphic and phase-separating compounds, yielding new physical insights that can guide the design of novel metastable materials. We further assert that not all low-energy metastable compounds can necessarily be synthesized, and propose a principle of 'remnant metastability'-that observable metastable crystalline phases are generally remnants of thermodynamic conditions where they were once the lowest free-energy phase.

High-Throughput Screening to Investigate the Relationship between the Selectivity and Working Capacity of Porous Materials for Propylene/Propane Adsorptive Separation

An efficient propylene/propane separation is a very critical process for saving the cost of energy in the petrochemical industry. For separation based on the pressure-swing adsorption process, we have screened ∼1 million crystal structures in the Cambridge Structural Database and Inorganic Crystal Structural Database with descriptors such as the surface area of N2, accessible surface area of propane, and pore-limiting diameter. Next, grand canonical Monte Carlo simulations have been performed to investigate the selectivities and working capacities of propylene/propane under experimental process conditions. Our simulations reveal that the selectivity and the working capacity have a trade-off relationship. To increase the working capacity of propylene, porous materials with high largest cavity diameters (LCDs) and low propylene binding energies (Qst) should be considered; conversely, for a high selectivity, porous materials with low LCDs and high propylene Qst should be considered, which leads to a trade-of...

Identification of solid oxygen‐containing Na‐electrolytes: An assessment based on crystallographic and economic parameters

We have scanned the inorganic crystal structure database using Voronoi‐Dirichlet methodology for inorganic, crystalline, solid Na electrolytes and applied a total of nine different crystallographic and economic parameters in order to evaluate the potential of each material. Especially for stationary electrochemical energy storage — used to counteract the capricious nature of renewable energy sources and momentary variations of energy consumption — Na‐based chemistries have a considerable market share. They rely on solid Na electrolytes separating the Na and S electrode compartments. We used data generated from the currently widest‐spread Na electrolytes to lay a foundation for the crystallographic data mining and Voronoi‐Dirichlet partitioning of the database. The structural data is the basis for the calculation of the above‐mentioned parameters. We introduced an evaluation and scoring scheme to systematise the results and — depending on the weighting scheme — point towards the most promising materials. Aluminosilicates and transition metal oxides seem especially interesting but, depending on the weighting, any of the more than 400 candidates could be the next‐generation solid Na electrolyte.

Machine Learning Energies of 2Million Elpasolite (ABC_{2}D_{6}) Crystals.

Elpasolite is the predominant quaternary crystal structure (AlNaK_{2}F_{6} prototype) reported in the Inorganic Crystal Structure Database. We develop a machine learning model to calculate density functional theory quality formation energies of all ∼2×10^{6} pristine ABC_{2}D_{6} elpasolite crystals that can be made up from main-group elements (up to bismuth). Our model's accuracy can be improved systematically, reaching a mean absolute error of 0.1 eV/atom for a training set consisting of 10×10^{3} crystals. Important bonding trends are revealed: fluoride is best suited to fit the coordination of the D site, which lowers the formation energy whereas the opposite is found for carbon. The bonding contribution of the elements A and B is very small on average. Low formation energies result from A and B being late elements from group II, C being a late (group I) element, and D being fluoride. Out of 2×10^{6} crystals, 90 unique structures are predicted to be on the convex hull-among which is NFAl_{2}Ca_{6}, with a peculiar stoichiometry and a negative atomic oxidation state for Al.

The optimal one dimensional periodic table: a modified Pettifor chemical scale from data mining

Starting from the experimental data contained in the inorganic crystal structure database, we use a statistical analysis to determine the likelihood that a chemical element A can be replaced by another B in a given structure. This information can be used to construct a matrix where each entry is a measure of this likelihood. By ordering the rows and columns of this matrix in order to reduce its bandwidth, we construct a one-dimension ordering of the chemical elements, analogous to the famous Pettifor scale. The new scale shows large similarities with the one of Pettifor, but also striking differences, especially in what comes to the ordering of the non-metals.

(Invited) Phosphors-By-Design: Developing the Next Generation of Luminescent Materials for Solid State Lighting

The development of rare-earth substituted phosphors generally relies on the chemical substitution of known compounds or searching phase-space to identify new materials. Yet, this approach often leads to the formation of known structure-types and incremental improvements of current luminescent materials. Transitioning beyond methods of classical materials discovery by turning to high-throughput computation and combinatorial algorithms has shown great promise in the development of new phosphors. A third method uses the combination of DFT-based computation and experiment to predict optical response. For example, calculating the Debye temperature and electronic band-gap of potential host compounds allows the selection of compounds from crystal structure databases ensuring only the best materials are experimentally explored. Our research has followed this approach to target a number of new luminescent materials ranging from borates to nitrides and showed an acceleration in materials discovery. Moreover, the complementary use of computation and synthesis provides an avenue for the fundamental understanding of the composition, structure, and property relationship necessary to advance the development of optical materials.

Crystal Structures, Surface Stability, and Water Adsorption Energies of La-Bastnäsite via Density Functional Theory and Experimental Studies

Bastnäsite is a fluoro-carbonate mineral that is the largest source of rare earth elements (REEs) such as Y, La, and Ce. With increasing demand for REE in many emerging technologies, there is an urgent need for improving the efficiency of ore beneficiation by froth flotation. To design improved flotation agents that can selectively bind to the mineral surface, a fundamental understanding of the bulk and surface properties of bastnäsite is essential. Unexpectedly, density functional theory (DFT) calculations using the PBEsol exchange correlation functional and the DFT-D3 dispersion correction reveal that the most stable form of La-bastnäsite is isomorphic to the structure of Ce-bastnäsite belonging to the P6̅2c space group, whereas the common structure listed in the Inorganic Crystal Structure Database structure belonging to the P6̅2m space group is ca. 11.3 kJ/mol higher in energy per LaFCO3 formula unit. We report powder X-ray diffraction measurements on synthetic La-bastnäsite to support these theoretical findings. Six different surfaces are studied by DFT, namely, [101̅0], [0001], [101̅1], [101̅2], [101̅4], and [112̅2]. Among these, the [101̅0] surface is the most stable with a surface energy of 0.73 J/m2 in vacuum and 0.45 J/m2 in aqueous solution. The shape of a La-bastnäsite nanoparticle is predicted via thermodynamic Wulff construction to be a hexagonal prism with [101̅0] and [0001] facets, chiseled at its ends by the [101̅1] and [101̅2] facets. The average surface energy of the nanoparticle in the gas phase is estimated to be 0.86 J/m2, in good agreement with a value of 1.11 J/m2 measured by calorimetry. The calculated adsorption energy of a water molecule varies widely with the surface plane and specific adsorption sites within each facet. The first layer of water molecules is predicted to adsorb strongly on the La-bastnäsite surface, in agreement with water adsorption calorimetry experiments. Our work provides an important step toward a detailed atomistic understanding of the bastnäsite–water interface and designing collector molecules that can bind specifically to bastnäsite.

Computational and experimental investigation for new transition metal selenides and sulfides: The importance of experimental verification for stability

Expanding the library of known inorganic materials with functional electronic or magnetic behavior is a longstanding goal in condensed matter physics and materials science. Recently, the transition metal chalchogenides including selenium and sulfur have been of interest because of their correlated-electron properties, as seen in the iron based superconductors and the transition metal dichalcogenides. However, the chalcogenide chemical space is less explored than that of oxides, and there is an open question of whether there may be new materials heretofore undiscovered. We perform a systematic combined theoretical and experimental search over ternary phase diagrams that are empty in the Inorganic Crystal Structure Database containing cations, transition metals, and one of selenium or sulfur. In these 27 ternary systems, we use a probabilistic model to reduce the likelihood of false negative predictions, which results in a list of 24 candidate materials. We then conduct a variety of synthesis experiments to check the candidate materials for stability. While the prediction method did obtain previously unknown compositions that are predicted stable within density functional theory, none of the candidate materials formed in our experiments. We come to the conclusion that these phase diagrams are "empty" in the case of bulk synthesis, but it remains a possibility that alternate synthesis routes may produce some of these phases.

Collaborative crystal structure prediction

The prediction of crystal structures is one of the most essential challenges in designing novel functional materials. A data-driven prediction technique that uses the database of known crystal structures and substitutes ions among materials of known crystal structures to concoct new crystal structures has been proposed. This technique has been applied to generate crystal-structure candidates for the purpose of first-principles-calculation-based high-throughput computational screening. However, this technique has a functional limitation that the ion substitution tendencies are available only for typical ions such that their associated crystal structures appear in well-known materials. To overcome such a limitation, this work introduces an idea of collaborative filtering to the calculation of the ionic substitution tendencies. Based on this idea, we develop symmetric matrix factorization (SMF) method to model underlying substitution conditions. In addition, we present a symmetric matrix co-factorization (SMCF) method to incorporate additional knowledge pertaining to chemical properties in estimating the substitution tendencies among ions with extremely small amount of previous knowledge in the database. The performance of the prediction is investigated along with existing techniques through in silico experiments using real crystal-structure database. The numerical results show that the proposed SMF- and SMCF-based prediction outperform existing techniques in terms of the prediction accuracy.

Prediction of new stable structure, promising electronic and thermodynamic properties of MoS3: Ab initio calculations

Abstract MoS3 has attracted considerable attention as potential hydrogen storage material due to the interaction between the hydrogen and unsaturated sulfur atoms. However, its structure and physical properties are unknown. By means of first-principles approach and Inorganic crystal structure Database (ISCD), we systematically investigated the structure, relevant physical and thermodynamic properties of MoS3. Phonon dispersion, electronic structure, band structure and heat capacity are calculated in detail. We predicted the orthorhombic B2ab (SrS3-type) and tetragonal P-421m (BaS3-type) structures of MoS3, which prefers to form the SrS3-type (Space group: B2ab, No.41) structure at the ground state. High pressure results in structural transition from SrS3-type structure to BaS3-type structure. This sulfide exhibits a degree of metallic behavior. The calculated heat capacity of MoS3 with SrS3-type structure is about of 39 J/(mol·K).

Building Blocks of Crystal Engineering: A Large-Database Study of the Intermolecular Approach between C–H Donor Groups and O, N, Cl, or F Acceptors in Organic Crystals

The nature of CH···X interactions in organic crystals, with X being an electronegative atom, has been the subject of extensive consideration with sometimes contradictory results and ensuing opinions. We perform statistical analysis on large databases of crystal structures retrieved from the Cambridge Structural Database. Crystals containing C–H donors only are considered in conjunction with each of O, N, Cl, or F acceptors in turn. The analysis of Coulombic polarization and dispersion components reveals that the lattice energies of these crystals are largely dominated by dispersive interactions. The frequency of short H···X contacts decreases through the series CHO > CHN > CHCl > CHF, being just sporadic in the latter. The presence of such contacts is positively correlated with the Coulombic contribution to molecule–molecule interaction energies but do not generally determine the pair energy. Short CH···O or CH···N contacts are often relegated to weakly bound pairs; their minor energy contributions might ...

Interactive and Versatile Navigation of Structural Databases.

We present CSD-CrossMiner, a novel tool for pharmacophore-based searches in crystal structure databases. Intuitive pharmacophore queries describing, among others, protein-ligand interaction patterns, ligand scaffolds, or protein environments can be built and modified interactively. Matching crystal structures are overlaid onto the query and visualized as soon as they are available, enabling the researcher to quickly modify a hypothesis on the fly. We exemplify the utility of the approach by showing applications relevant to real-world drug discovery projects, including the identification of novel fragments for a specific protein environment or scaffold hopping. The ability to concurrently search protein-ligand binding sites extracted from the Protein Data Bank (PDB) and small organic molecules from the Cambridge Structural Database (CSD) using the same pharmacophore query further emphasizes the flexibility of CSD-CrossMiner. We believe that CSD-CrossMiner closes an important gap in mining structural data and will allow users to extract more value from the growing number of available crystal structures.

Pyridine N-oxides as coformers in the development of drug cocrystals

Pyridine N-oxides were synthesized via a convenient method and exploited in the preparation of drug cocrystals. Drugs associated with aqueous solubility issues such as propofol, ferulic acid, sulfathiazole, p-aminobenzoic acid etc. were used as the representative active ingredients to engineer pharmaceutical solids of a desired phase. In this study, 4,4′-bipyridine-N,N′-dioxide was picked as the cocrystal former. The types of supramolecular heterosynthons exhibited by the binary systems of N-oxide·drugs were analyzed. The formation of hydrogen bond synthons such as COOH–pyridine N-oxide, OH or NH–pyridine N-oxide was found to be robust and followed the trend observed in the Crystal Structure Database. These synthons were further correlated with the ameliorated properties of the drugs, which was supported by experiments, DFT studies and Hirshfeld surface analysis. This has been a goal in drug development.

‘Bad’ distributions of good data: unusual statistics of structural databases

Distributions of data taken from crystal structure databases, display unusual statistical properties like non-Gaussian shape, polymodality, and heavy tails. These features, typical for statistics of numerical data in social systems, appear in bigger sets (from hundreds to many thousand points) of database-originated parameters. The non-classic statistics of physical data collected through many years reflects a strong impact of social factors (financial support, exchange of information, competition, etc.) on a research activity. The values of some definite structural parameter, determined (and deposited to a database) by different authors, generally are neither independent nor random; their handling by common statistical tools may result in incorrect conclusions and wrong predictions. These statements are illustrated by several sets of reliable structural data whose statistics looks ‘bad,’ or inconclusive, in contemporary structural chemistry.

The crystal chemistry of inorganic metal borohydrides and their relation to metal oxides

The crystal structures of inorganic homoleptic metal borohydrides are analysed with respect to their structural prototypes found amongst metal oxides in the inorganic databases such as Pearson's Crystal Data [Villars & Cenzual (2015). Pearson's Crystal Data. Crystal Structure Database for Inorganic Compounds, Release 2014/2015, ASM International, Materials Park, Ohio, USA]. The coordination polyhedra around the cations and the borohydride anion are determined, and constitute the basis of the structural systematics underlying metal borohydride chemistry in various frameworks and variants of ionic packing, including complex anions and the packing of neutral molecules in the crystal. Underlying nets are determined by topology analysis using the program TOPOS [Blatov (2006). IUCr CompComm. Newsl. 7, 4-38]. It is found that the Pauling rules for ionic crystals apply to all non-molecular borohydride crystal structures, and that the latter can often be derived by simple deformation of the close-packed anionic lattices c.c.p. and h.c.p., by partially removing anions and filling tetrahedral or octahedral sites. The deviation from an ideal close packing is facilitated in metal borohydrides with respect to the oxide due to geometrical and electronic considerations of the BH4(-) anion (tetrahedral shape, polarizability). This review on crystal chemistry of borohydrides and their similarity to oxides is a contribution which should serve materials engineers as a roadmap to design new materials, synthetic chemists in their search for promising compounds to be prepared, and materials scientists in understanding the properties of novel materials.

The Open Quantum Materials Database (OQMD): assessing the accuracy of DFT formation energies

AbstractThe Open Quantum Materials Database (OQMD) is a high-throughput database currently consisting of nearly 300,000 density functional theory (DFT) total energy calculations of compounds from the Inorganic Crystal Structure Database (ICSD) and decorations of commonly occurring crystal structures. To maximise the impact of these data, the entire database is being made available, without restrictions, at www.oqmd.org/download. In this paper, we outline the structure and contents of the database, and then use it to evaluate the accuracy of the calculations therein by comparing DFT predictions with experimental measurements for the stability of all elemental ground-state structures and 1,670 experimental formation energies of compounds. This represents the largest comparison between DFT and experimental formation energies to date. The apparent mean absolute error between experimental measurements and our calculations is 0.096 eV/atom. In order to estimate how much error to attribute to the DFT calculations, we also examine deviation between different experimental measurements themselves where multiple sources are available, and find a surprisingly large mean absolute error of 0.082 eV/atom. Hence, we suggest that a significant fraction of the error between DFT and experimental formation energies may be attributed to experimental uncertainties. Finally, we evaluate the stability of compounds in the OQMD (including compounds obtained from the ICSD as well as hypothetical structures), which allows us to predict the existence of ~3,200 new compounds that have not been experimentally characterised and uncover trends in material discovery, based on historical data available within the ICSD.