Crystal Structure Database Research Articles

Analysis of supramolecular interactions in alendroniate alkali metal salts: synthesis, structure, and properties of novel sodium alendronate polymorph

A new polymorph of anhydrous sodium alendronate, C4H12NO7P2Na, has been synthesized and characterized by single crystal X-ray diffraction as well as infrared spectroscopy and thermal analysis. The title compound crystallizes in the monoclinic P21/c space group. Asymmetric unit consists of one alendronic anion and one sodium cation. An interplay of classical strong O-H…O, N-H…O and non-classical weak C-H…O hydrogen bonds creates 3D framework in the crystal. Contrary to previously reported sodium alendronate salts, in which Na+ cation is surrounded by six-coordinated sphere, in compound (1), the Na+ cation is five-coordinated in a distorted trigonal-bipyramidal geometry. In order to provide a detailed investigation of the molecular arrangement in view of intermolecular interactions, the title compound was compared with alendronic acid and other known alkali metal alendronate salts, retrieved from the Cambridge Crystal Structure Database. The intercontacts were qualitatively and quantitatively compared using Hirshfeld surface analysis. It highlights that strong O…H/H…O and subtle H…H contacts play an influential role in the total surface area. The Me+…H/H…Me+ and Me+…O/O…Me+ contacts are meaningful as well. These evidently simple systems show a diverse complexity. Moreover, the powder X-ray diffraction, DSC, thermogravimetry/derivative thermogravimetry, and FT-IR results are also reported.

Extremely Strong Halogen Bond. The Case of a Double-Charge-Assisted Halogen Bridge.

The stable model of a double (±)charge-assisted halogen bridge has been built on the basis of searches of the Crystal Structure Database. The model, investigated by DFT theory, consists of quinuclidine-like cation derivatives and a set of simple anions. These charged fragments form halogen-bonded complexes of which the energy of complexation in some cases reaches 100 kcal/mol. Even for such strong interactions, the QTAIM characteristics are similar to those of the more classic, relatively weak halogen bonds. An important effect of complexation is the charge transfer measured by means of QTAIM and NBO. It can also be supposed, on the basis of detailed structural and QTAIM analysis, that the delocalization of the charge in a quinuclidine moiety occurs through space and not necessarily along formal bonds. The analysis of only partially charged and fully neutral counterparts of a double (±)charge-assisted halogen bridge shows significantly weaker bonding, being less than 10 kcal/mol.

Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds.

This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget, and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and grasp the types of calculations used in protein target fishing. In addition, we review the main features of these methods, programs and databases and provide a variety of examples illustrating the application of one or a combination of reverse screening methods for accurate target prediction.

AFLOW-SYM: platform for the complete, automatic and self-consistent symmetry analysis of crystals.

Determination of the symmetry profile of structures is a persistent challenge in materials science. Results often vary amongst standard packages, hindering autonomous materials development by requiring continuous user attention and educated guesses. This article presents a robust procedure for evaluating the complete suite of symmetry properties, featuring various representations for the point, factor and space groups, site symmetries and Wyckoff positions. The protocol determines a system-specific mapping tolerance that yields symmetry operations entirely commensurate with fundamental crystallographic principles. The self-consistent tolerance characterizes the effective spatial resolution of the reported atomic positions. The approach is compared with the most used programs and is successfully validated against the space-group information provided for over 54 000 entries in the Inorganic Crystal Structure Database (ICSD). Subsequently, a complete symmetry analysis is applied to all 1.7+ million entries of the AFLOW data repository. The AFLOW-SYM package has been implemented in, and made available for, public use through the automated ab initio framework AFLOW.

Comparing side chain packing in soluble proteins, protein‐protein interfaces, and transmembrane proteins

We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins.

Computational Screening of Hydration Reactions for Thermal Energy Storage: New Materials and Design Rules

The implementation of thermal energy storage (TES) can improve the efficiency of existing industrial processes, and enable new applications that require the uptake/release of heat on-demand. Among the myriad strategies for TES, thermochemical hydration/dehydration reactions are arguably the most promising due to their high energy densities, simplicity, cost effectiveness, and potential for reversibility at moderate temperatures. The present study uses first-principles calculations to identify TES materials that can out-perform known compounds. High-throughput density functional theory calculations were performed on metal halide hydrates and hydroxides mined from the Inorganic Crystal Structure Database. In total, 265 hydration reactions were characterized with respect to their thermodynamic properties, gravimetric and volumetric energy densities, and operating temperatures. Promising reactions were identified for three temperature ranges: low ( 300 °C). Several hig...

High-Throughput Computational Assessment of Previously Synthesized Semiconductors for Photovoltaic and Photoelectrochemical Devices

Using computational screening we identify materials with potential use as light absorbers in photovoltaic or photoelectrochemical devices. The screening focuses on compounds of up to three different chemical elements which are abundant and nontoxic. A prescreening is carried out based on information from the Inorganic Crystal Structure Database and Open Quantum Materials Database. The light absorption, carrier mobility, defect tolerance, and stability of the materials are assessed by a set of simple computational descriptors. The identified 74 materials include a variety of pnictogenides, chalcogenides, and halides. Several recently investigated light absorbers, such as CsSnI3, CsSnBr3, and BaZrS3, appear on the list.

Matrix- and tensor-based recommender systems for the discovery of currently unknown inorganic compounds

Chemically relevant compositions (CRCs) and atomic arrangements of inorganic compounds have been collected as inorganic crystal structure databases. Machine-learning is a unique approach to search for currently unknown CRCs from vast candidates. Herein we propose matrix- and tensor-based recommender system approaches to predict currently unknown CRCs from database entries of CRCs. Firstly, the performance of the recommender system approaches to discover currently unknown CRCs is examined. A Tucker decomposition recommender system shows the best discovery rate of CRCs as the majority of the top 100 recommended ternary and quaternary compositions correspond to CRCs. Secondly, systematic density functional theory (DFT) calculations are performed to investigate the phase stability of the recommended currently unknown CRCs. The phase stability of the 27 compositions reveals that 23 currently unknown compounds are stable. These results indicate that the recommender system has great potential to accelerate the discovery of new compounds.

Crystallochemical tools in the search for cathode materials of rechargeable Na-ion batteries and analysis of their transport properties

In this work, we present a combined approach comprising of crystallochemical methods such as Voronoi-Dirichlet partition (VDP), bond valence sums mapping (BVSM) and bond valence energy landscapes (BVEL) for the search for Na-ion cathode materials. Using this approach a systematic screening of the inorganic crystal structure database (ICSD-2016/2) was performed to extract potential cathode materials for Na-ion batteries. As a result, a down-selected and reviewed list of known and newly discovered cathode materials compared and characterized structurally with a special focus on Na+ mobility properties revealed by crystallochemical methods is given. DFT calculations were also carried out for a number of materials to validate the screening algorithm, applicability and reliability of the crystallochemical approaches as well as to get a deeper insight on the Na+ diffusion properties.

Comparison of approximations in density functional theory calculations: Energetics and structure of binary oxides

High-throughput first-principles calculations based on density functional theory (DFT) are a powerful tool in data-oriented materials research. The choice of approximation to the exchange-correlation functional is crucial as it strongly affects the accuracy of DFT calculations. This study compares performance of seven approximations, six of which are based on Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) with and without Hubbard U and van der Waals corrections (PBE, PBE+U, PBED3, PBED3+U, PBEsol, and PBEsol+U), and the strongly constrained and appropriately normed (SCAN) meta-GGA on the energetics and crystal structure of elementary substances and binary oxides. For the latter, only those with closed-shell electronic structures are considered, examples of which include $\mathrm{C}{\mathrm{u}}_{2}\mathrm{O}$, $\mathrm{A}{\mathrm{g}}_{2}\mathrm{O}$, MgO, ZnO, CdO, SnO, PbO, $\mathrm{A}{\mathrm{l}}_{2}{\mathrm{O}}_{3}$, $\mathrm{G}{\mathrm{a}}_{2}{\mathrm{O}}_{3}$, $\mathrm{I}{\mathrm{n}}_{2}{\mathrm{O}}_{3}$, $\mathrm{L}{\mathrm{a}}_{2}{\mathrm{O}}_{3}$, $\mathrm{B}{\mathrm{i}}_{2}{\mathrm{O}}_{3}$, $\mathrm{Si}{\mathrm{O}}_{2}$, $\mathrm{Sn}{\mathrm{O}}_{2}$, $\mathrm{Pb}{\mathrm{O}}_{2}$, $\mathrm{Ti}{\mathrm{O}}_{2}$, $\mathrm{Zr}{\mathrm{O}}_{2}$, $\mathrm{Hf}{\mathrm{O}}_{2}$, ${\mathrm{V}}_{2}{\mathrm{O}}_{5}$, $\mathrm{N}{\mathrm{b}}_{2}{\mathrm{O}}_{5}$, $\mathrm{T}{\mathrm{a}}_{2}{\mathrm{O}}_{5}$, $\mathrm{Mo}{\mathrm{O}}_{3}$, and $\mathrm{W}{\mathrm{O}}_{3}$. Prototype crystal structures are selected from the Inorganic Crystal Structure Database (ICSD) and cation substitution is used to make a set of existing and hypothetical oxides. Two indices are proposed to quantify the extent of lattice and internal coordinate relaxation during a calculation. The former is based on the second invariant and determinant of the transformation matrix of basis vectors from before relaxation to after relaxation, and the latter is derived from shifts of internal coordinates of atoms in the unit cell. PBED3, PBEsol, and SCAN reproduce experimental lattice parameters of elementary substances and oxides well with few outliers. Notably, PBEsol and SCAN predict the lattice parameters of low dimensional structures comparably well with PBED3, even though these two functionals do not explicitly treat van der Waals interactions. SCAN gives formation enthalpies and Gibbs free energies closest to experimental data, with mean errors (MEs) of 0.01 and \ensuremath{-}0.04 eV, respectively, and root-mean-square errors (RMSEs) are both 0.07 eV. In contrast, all GGAs including those with Hubbard U and van der Waals corrections give 0.1 to 0.2 eV MEs and at least 0.11 eV RMSEs. Phonon contributions of solid phases to the formation enthalpies and Gibbs free energies are estimated to be small at less than \ensuremath{\sim}0.1 eV/atom within the quasiharmonic approximation. The same crystal structure appears as the lowest energy polymorph with different approximations in most of the investigated binary oxides. However, there are some systems where the choice of approximation significantly affects energy differences between polymorphs, or even the order of stability between phases. SCAN is the most reasonable regarding relative energies between polymorphs. The calculated transition pressure between polymorphs of ZnO and $\mathrm{Sn}{\mathrm{O}}_{2}$ is closest to experimental values when PBED3, PBEsol (also PBED3+U and PBEsol+U for ZnO), and SCAN are employed. In summary, SCAN appears to be the best choice among the seven approximations based on the analysis of the energetics and crystal structure of binary oxides, while PBEsol is the best among the GGAs considered and shows a comparably good performance with SCAN for many cases. The use of PBEsol+U alongside PBEsol is also a reasonable choice, given that U corrections are required for several materials to qualitatively reproduce their electronic structures.

Reactivity of 12-tungstophosphoric acid and its inhibitor potency toward Na+/K+-ATPase: A combined 31P NMR study, ab initio calculations and crystallographic analysis

Influence of 12-tungstophosphoric acid (WPA) on conversion of adenosine triphosphate (ATP) to adenosine diphosphate (ADP) in the presence of Na+/K+-ATPase was monitored by 31P NMR spectroscopy. It was shown that WPA exhibits inhibitory effect on Na+/K+-ATPase activity. In order to study WPA reactivity and intermolecular interactions between WPA oxygen atoms and different proton donor types (D=O, N, C), we have considered data for WPA based compounds from the Cambridge Structural Database (CSD), the Crystallographic Open Database (COD) and the Inorganic Crystal Structure Database (ICSD). Binding properties of Keggin's anion in biological systems are illustrated using Protein Data Bank (PDB). This work constitutes the first determination of theoretical Bader charges on polyoxotungstate compound via the Atom In Molecule theory. An analysis of electrostatic potential maps at the molecular surface and charge of WPA, resulting from DFT calculations, suggests that the preferred protonation site corresponds to WPA bridging oxygen. These results enlightened WPA chemical reactivity and its potential biological applications such as the inhibition of the ATPase activity.

Germanene and stanene on two-dimensional substrates: Dirac cone and Z2 invariant

By using the combination of the ab initio density functional theory and data mining of the Inorganic Crystal Structure Database, a series of monolayer materials are found to be suitable substrates for germanene or stanene, including some of the $\mathrm{Cd}{\mathrm{I}}_{2}$-type materials, CuI, and GaGeTe. All of the found materials, when they are used as the substrate, can almost preserve the quasifreestanding geometry, stability, and band structure of germanene or stanene. Among them, $\mathrm{Cd}{\mathrm{I}}_{2}$ and $\mathrm{Zn}{\mathrm{I}}_{2}$ can open a relatively large band gap of 0.16--0.18 (0.13--0.16) eV [without (with) spin-orbit coupling] in germanene, while preserving Dirac-cone-like band structures. Moreover, the ${Z}_{2}$ invariants of germanene on CuI and stanene on $\mathrm{Ca}{\mathrm{I}}_{2}$ are found to be nontrivial. The interaction between germanene and substrates can be well modeled by the low-energy tight-binding Hamiltonian of germanene under external fields. Our analysis based on the tight-binding Hamiltonian shows that suitable substrates mainly act like a ``pseudoelectric'' field on germanene, and that strong linear correlations are seen among the ``pseudoelectric'' field, extrinsic Rashba coefficient, and charge transfer.

How Chemical Composition Alone Can Predict Vibrational Free Energies and Entropies of Solids

Computing vibrational free energies (Fvib) and entropies (Svib) has posed a long-standing challenge to the high-throughput ab initio investigation of finite temperature properties of solids. Here, we use machine-learning techniques to efficiently predict Fvib and Svib of crystalline compounds in the Inorganic Crystal Structure Database. Using descriptors based simply on the chemical formula and using a training set of only 300 compounds, mean absolute errors of less than 0.04 meV/K/atom (15 meV/atom) are achieved for Svib (Fvib), whose values are distributed within a range of 0.9 meV/K/atom (300 meV/atom.) In addition, for training sets containing fewer than 2000 compounds, the chemical formula alone is shown to perform as well as, if not better than, four other more complex descriptors previously used in the literature. The accuracy and simplicity of the approach means that it can be advantageously used for fast screening of chemical reactions at finite temperatures.

Predicting the Thermodynamic Stability of Solids Combining Density Functional Theory and Machine Learning

We perform a large scale benchmark of machine learning methods for the prediction of the thermodynamic stability of solids. We start by constructing a data set that comprises density functional theory calculations of around 250000 cubic perovskite systems. This includes all possible perovskite and antiperovskite crystals that can be generated with elements from hydrogen to bismuth, excluding rare gases and lanthanides. Incidentally, these calculations already reveal a large number of systems (around 500) that are thermodynamically stable but that are not present in crystal structure databases. Moreover, some of these phases have unconventional compositions and define completely new families of perovskites. This data set is then used to train and test a series of machine learning algorithms to predict the energy distance to the convex hull of stability. In particular, we study the performance of ridge regression, random forests, extremely randomized trees (including adaptive boosting), and neural networks....

Crystal structure databases to have single portal

Two of the main crystallographic structure databases, the Cambridge Structural Database (CSD) and the Inorganic Crystal Structure Database (ICSD), will have a single portal for users to deposit and search for data starting later this year, their operating organizations announced on March 27. CSD contains 875,000 entries for organic and metal-organic species and is operated by the Cambridge Crystallographic Data Centre in England. ICSD contains 187,000 inorganic structures and is operated by FIZ Karlsruhe—Leibniz Institute for Information Infrastructure. The ability to search both databases simultaneously “will be of tremendous value for researchers, especially those that work at the interface of organic, inorganic, and coordination chemistry,” comments Tomislav Friscic, a chemistry professor at McGill University and a member of the governing council of the American Crystallographic Association. “Modern chemical science is all about crossing borders and interfaces, so this is really a constructive and time...

Morphology-dependent electrocatalytic performance of Fe2(MoO4)3 for electro-oxidation of methanol in alkaline medium

Electrochemically synthesized nanosphere, nanorod and nanotube Fe2(MoO4)3 at optimized temperature and current density are characterized with XRD, SEM, TEM, XPS. Crystal lattices of the three types Fe2(MoO4)3 detected by HRTEM are well matched with the simulation analysis results from Materials Studio 6.0 based on the inorganic crystal structure database (ICSD) data and the modified XRD lattice parameters. The ratios of Fe/Mo on the surface resulted from XPS analysis are 1.47, 1.63 and 2.22 respectively for nanosphere, nanorod and nanotube. The mixture of Fe2(MoO4)3 with polytetrafluoroethylene dispersion are coated on glass carbon substrate as electrode for electrocatalytic performance test by cyclic voltammetries in 0.1 mol/L KOH and 1 mol/L methanol electrolyte. Methanol oxidation peak current density of the Nanotube- Fe2(MoO4)3/GCEs electrode is 3.27 mA/cm2 higher than 2.8 mA/cm2 of platinum foil electrode, which shows enhanced catalytic activity of Nanotube-Fe2(MoO4)3/GCEs. The cyclic stability in terms of peak current retention are 91%, 92% and 88% respectively for Nanosphere-Fe2(MoO4)3/GCE, Nanorod-Fe2(MoO4)3/GCE and Nanotube-Fe2(MoO4)3/GCE electrode after 220 cycles. It is concluded that nanosized Fe2(MoO4)3 could be promising alternative non-noble electro-catalysts for electro-oxidation of methanol in alkaline medium.

Structural landscape of base pairs containing post-transcriptional modifications in RNA.

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA.

Rediscovering the Crystal Chemistry of Borides

For decades, borides have been primarily studied as crystallographic oddities. With such a wide variety of structures (a quick survey of the Inorganic Crystal Structure Database counts 1253 entries for binary boron compounds!), it is surprising that the applications of borides have been quite limited despite a great deal of fundamental research. If anything, the rich crystal chemistry found in borides could well provide the right tool for almost any application. The interplay between metals and the boron results in even more varied material's properties, many of which can be tuned via chemistry. Thus, the aim of this review is to reintroduce to the scientific community the developments in boride crystal chemistry over the past 60 years. We tie structures to material properties, and furthermore, elaborate on convenient synthetic routes toward preparing borides.

Planarity of substituted pyrrole and furan rings in (3R*, 1′S*, 3′R*)-3-(1′-tert-butylamino-1′H, 3′ H-benzo[c]furan-3′-yl)-2-tert-butyl-2,3-dihydro-1H-benzo[c]pyrrol-1-one

Abstract The title structure, (3R*, 1′S*, 3′R*)-3-(1′-tert-butylamino-1′H,3′H-benzo[c]furan-3′-yl)-2-tert-butyl-2,3-dihydro-1H-benzo[c]pyrrol-1-one has been determined at 290 and 150 K by single-crystal X-ray diffraction. The structure comprises two symmetry independent molecules with very similar conformations which differ mostly by orientations of the tert-butyl groups, situated at the periphery of these molecules. The molecules are composed of two parts, the cores of which are isoindolinone and isobenzofuran rings being bound by C–C bonds. The planarities of the pyrrolone and furan rings are compared with the known structures retrieved from the Cambridge Crystal Structure Database. It transpires in the title molecules, the planarity of the carbonyl-substituted pyrrole rings is exceptionally distorted in contrast to the furan rings. This fact is just the opposite of the tendency inferred from the Cambridge Crystal Structure Database. The reason may be the influence of the voluminous tert-butyl group which is attached to the nitrogen of the pyrrole group, as well as short centroid–centroid distances between the carbonyl-substituted pyrrole and furan rings. Cohesion forces between the molecules and their parts are provided by weak interactions only: The packing suggests C–H···O, π–π-electron ring interactions, N–H···π-electron ring as well as C–H···π-electron ring interactions. The structure determination of the title compound, the product of the reaction of o-phthalaldehyde with tert-butylamine, has provided indication about the mechanism of a chemical reaction which resulted in the formation of the title molecule.

Topology-Scaling Identification of Layered Solids and Stable Exfoliated 2D Materials.

The Materials Project crystal structure database has been searched for materials possessing layered motifs in their crystal structures using a topology-scaling algorithm. The algorithm identifies and measures the sizes of bonded atomic clusters in a structure's unit cell, and determines their scaling with cell size. The search yielded 826 stable layered materials that are considered as candidates for the formation of two-dimensional monolayers via exfoliation. Density-functional theory was used to calculate the exfoliation energy of each material and 680 monolayers emerge with exfoliation energies below those of already-existent two-dimensional materials. The crystal structures of these two-dimensional materials provide templates for future theoretical searches of stable two-dimensional materials. The optimized structures and other calculated data for all 826 monolayers are provided at our database (https://materialsweb.org).