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The structures with different compositions of the binary Mg–Y alloys have been predicted by first-principles calculations combined with an unbiased Crystal structure Analysis by Particle Swarm Optimization (CALYPSO) structure searching method. The two already known stoichiometries alloys of Mg1Y1 with Pm- 3 m symmetry and Mg3Y1 with Fm- 3 m are confirmed, and a new stoichiometry alloy of Mg1Y3 with P 2 / m symmetry is proposed. The dynamical and mechanical stabilities for the three alloys at different pressures are investigated by phonon spectra and mechanical stability criteria, respectively. Subsequently, the bulk modulus, shear modulus, Young's modulus, the brittleness/ductile behavior, the elastic anisotropy as well as Vickers hardness for the three alloys at 0 GPa are discussed in detail. The results show that the Mg1Y1, Mg3Y1 and Mg1Y3 alloys improve the hardness and stiffness compared with pure Mg, and Mg1Y3 alloy is of the best ductility in the three alloys. Meanwhile, the three alloys exhibit anisotropic. Moreover, the thermodynamic properties, such as Debye temperature, heat capacity at constant volume, entropy and Helmholtz free energy for the three stable alloys, are predicted and discussed. [ABSTRACT FROM AUTHOR]

We have systematically explored the crystal structures of alkaline-earth metal sulfides under pressure by using a swarm-intelligence structural prediction method. At low pressures we successfully reproduced their known structures and phase transition sequences. Under high pressure, MgS is predicted to transform from B28 to a β -NbP-type structure at 262 GPa. CaS and SrS present the same phase transition sequence, from B2 to a β -NbP-type structure, while BaS is predicted to transform to a Imma structure. The Imma structure is actually similar to the β -NbP-type structure, as it can be seen as a modulated distortion of the latter structure. The absence of any imaginary phonon mode for the predicted structures suggests that they are dynamically stable. The calculated electronic band structures and density of states reveal that all the predicted phases are metallic, except that MgS is a semiconductor. Subsequent electron-phonon coupling calculations suggest that Imma BaS is a superconductor with a low T _c of 1.32 K, while β -NbP MgS, CaS and SrS are not superconductors. The current study provides a comprehensive analysis of phase transitions for alkaline-earth metal sulfides up to 300 GPa and might stimulate experimental studies in the future.

The structure, phase stability, and elastic properties of Ta 2 B have been carefully investigated by density functional theory. We propose a new orthorhombic Cmcm structure that is more stable than the previous I 4/ mcm. Combined with a study of the relationship between enthalpy pressure and convex hull, the Cmcm structure is found to be stable at atmospheric pressure and, at zero pressure, the stable phases are Ta 2 B, TaB, Ta 3 B 4 , Ta 5 B 6 , and TaB 2 , in agreement with experimental results. Above a pressure of 60 GPa, Ta 2 B becomes unstable. • A new stable Cmcm structure of Ta 2 B is uncovered. • Phonon dispersions and elastic constant analysis suggest that the Cmcm -Ta 2 B is stable at ambient condition. • The new Cmcm -Ta 2 B is energetically much superior to the previously proposed I 4/ mcm structure. [ABSTRACT FROM AUTHOR]

We use first-principles density functional theory to conduct an extensive structure search using the AIRSS package for elemental sulfur in the range 50–550 GPa. We then obtain the low-temperature phase diagram of sulfur in the same pressure range, including vibrational effects through the harmonic approximation. We do not find any structures lower in energy than those already reported in experiment, although the phase diagram below 100 GPa is found to be crowded with structures separated by only a few meV. We report the transition sequence $I{4}_{1}/{acd}\to P\bar{1}\to $ ICM $\to \,C2/m\to R\bar{3}m\to Im\bar{3}m$ and obtain accurate pressures for each transition, although we find the second-order $C2/m\to R\bar{3}m$ transition particularly difficult to define. Contrary to previous first-principles works (Pavel et al ; Rudin and Liu 1999 Phys. Rev. Lett. 83 3049–52), we do not reproduce a trigonal $\to $ simple cubic transition at either the static lattice or harmonic level. We also undertake a detailed analysis of the incommensurately modulated (ICM) phase of sulfur phase using a commensurate approximant found in the structure search. We find that the modulation amplitude is zero above 96 GPa; some 40 GPa below the experimentally reported transition to the unmodulated phase. We find that the body-centred atoms in the relaxed ICM approximant are, in addition to the dominant transverse modulation (which is a frozen-in optical phonon mode), slightly displaced longitudinally in the b -direction. We subsequently discover that this (small) longitudinal modulation is coupled to the transverse mode, and hence report previously unnoticed weak-mode coupling between transverse and longitudinal optical phonons in the ICM phase.

Structure-based patent searching with high precision and recall is the most important information request in chemistry. The different parts of chemical patent information are stored in different databases and the challenge is to bring the different parts together in a consistent manner and retrieve a complete set of structures and patents. With the application of set theory, it is possible to develop a method which enables the user to obtain a group of corresponding, consistent answer sets after subsequent searching in the different databases and utilizing the special features of both structure and concept searching. A second goal of this paper is to demonstrate the relevance of Markush structures for patent searches in a quantitative manner. Another goal is the development of a set of simple indicators which can be applied to the search results of structure-based patent searches. Four indicators have been chosen with special focus on the relevance of Markush structures for patent searches. The searches and the analysis were carried out with ten pharmaceutical examples. The results show in a quantitative manner, that a search in the Markush database yields a number of inventions (patent families) that cannot be found via searches in specific structure databases alone. [ABSTRACT FROM AUTHOR]

The ultra-long relaxation time of glass transition makes it difficult to construct atomic models of amorphous materials by conventional methods. We propose a novel method for building such atomic models using data assimilation method by simulated annealing with an accurately computed interatomic potential augmented by penalty from experimental data. The advantage of this method is that not only can it reproduce experimental data as the structure refinement methods like reverse Monte Carlo but also obtain the reasonable structure in terms of interatomic potential energy. In addition, thanks to the interatomic potential, we do not need high Q range diffraction data, which is necessary to take into account the short-range order. Persistent homology analysis shows that the amorphous ice obtained by the new method is indeed more ordered at intermediate range. • A new method for structural search of glasses using experimental data. • Atomic models obtained are consistent with experiment AND energetically stable. • Strong improvement of the treatment of incomplete experimental data of glasses. [ABSTRACT FROM AUTHOR]

The structural stabilities of TiB 3 under high pressure have been studied by using first-principle calculations. Results show that TiB 3 transforms from the C 2/ m phase to P 2/ m phase at 74.7 GPa. The C 2/ m -TiB 3 and the high-pressure P 2/ m -TiB 3 are all hard materials, with hardnesses of 46.7 GPa and 45 GPa calculated at atmospheric pressure, respectively. As can be seen, the negative formation enthalpies suggest that they are stable and could be synthesised at atmospheric pressure. The ELF calculations reveal that there are very strong covalent bonds between the boron atoms in both phases, and this is an important reason for the high hardness. Moreover, the mechanical properties of TiB 3 in the two phases are discussed. • A new stable high pressure P 2/ m structure of TiB 3 is uncovered. • Phonon dispersions and elastic constant analysis suggest that the P 2/ m -TiB 3 is stable at ambient condition. • The new P 2/ m -TiB 3 has a high hardness of 45 GPa and can be considered a superhard material. [ABSTRACT FROM AUTHOR]

We present two distorted face-centered cubic (dfcc) structures of yttrium under high pressure, which have been found by a first-principles genetic algorithm technique. The structures are a tetragonalP43(dfcc-I) and a triclinicP1¯ (dfcc-II), formed by slight distortions from a trigonalR3¯mstructure reported as the dfcc phase earlier. The enthalpy difference between the two dfcc structures is less than 0.2 mRy/atom, and dfcc-I is marginally more stable than dfcc-II in lower pressure region. The enthalpy comparison among candidate structures indicates the structural phase transitions into dfcc-I at 41 GPa, into dfcc-II at 81 GPa, and into an orthorhombicFdddstructure at 106 GPa. [ABSTRACT FROM PUBLISHER]

• A computational approach based on density functional and random structure searching to investigate the structures of mono- and bi-bimetallic nanoclusters and the CO 2 activation was proposed. • Low-symmetry amorphous pure copper clusters have higher catalytic activity than high-symmetry icosahedral nanoclusters. • The activation of CO 2 on nanoclusters was characterised using energetic, structural, and electronic properties. • The free energy pathways of CO 2 -to-CO and hydrogen evolution reaction were computed to predict the optimal copper and copper-metallic nanocatalysts. Understanding the effect of nano-structuring and metal doping on the properties of copper-based clusters is crucial to developing effective catalysts for the electrochemical conversion of CO 2 to value-added chemicals. We present a computational approach based on density functional and random structure searching to investigate the structures of mono- and bi-bimetallic nanoclusters, the activation of CO 2 on the catalyst, and the mechanism of CO 2 dissociation. We have applied this approach to predict the structure and catalytic properties of Cu n (n = 1–55) and (Cu-M) m (M = Fe, Sn, Zn with 1 ≤ m ≤ 27) nanoclusters. We also considered the CO 2 activation and conversion on the low index Cu and Cu-M (100) surfaces, and high-symmetry (icosahedral) and core-shell Cu-M clusters. The most stable clusters are low-symmetry pure copper clusters with an amorphous character. Also, these clusters have higher catalytic activity than Cu (100) and high-symmetry icosahedral nanoclusters. In both pure copper and bimetallic systems, the physiosorbed state of CO 2 is the most stable and energy is required to activate the molecule. The stabilization of the chemisorbed state occurs in systems such as Cu-Fe where there is delocalization of orbitals around the Fermi level, causing the large charge transfer from the catalyst to CO 2. We have also conducted calculations of the free energy profiles of the CO 2 -to-CO conversion and the competitive hydrogen evolution reaction. The CO 2 reduction reaction is dominant over the hydrogen evolution reaction on the Cu randomly generated cluster due to the lower potential limiting step. Among other considered bimetallic, the core@shell models also display good catalytic activity and selectivity towards the CO 2 reduction reaction. This work identifies insightful structure-property relationships for CO 2 activation, highlighting the influence of size and composition on the CO 2 activation and intermediate stability in designing catalytic cupper-based mono- and bi-metallic clusters for the CO 2 reduction reaction. We propose a computational approach to investigate the structures of copper-based nanoclusters, the activation of CO 2 on the catalyst, and the mechanism of CO 2 -to-CO conversion. The results show that low-symmetry pure copper clusters with an amorphous character are particularly active in the CO 2 reduction reaction without being poisoned by the competitive hydrogen evolution reaction. [Display omitted] [ABSTRACT FROM AUTHOR]

SUMMARY Protein structure comparison is a vital process in several tasks like the prediction of protein structures and functions and detecting the proteins evolutionary relationships. The expansion of both the parallel computational hardware and the discovered protein structures stimulates the growth of the parallel computational tools to handle this massive data of proteome. Here, we present a parallel tool, parallel 3D-BLAST (PAR-3D-BLAST), which lists the similar structures to the query protein. Each protein in the result list has a structural similarity score and an alignment to the query structure. The presented tool is implemented to fit both the standalone multi-core computers and clusters of multi-core nodes. The achieved speedup is linear and scalable. The experimental results outline that the speedup increases as the size of the database increases. Using a cluster of 35 computing cores, the tool constructs the database of the entire structural classification of proteins dataset, 108,116 protein entries, in less than 6min and with average query time of 1.45s. The obtained speed up is 20 times for database construction and 17 times for searching the query. The tool is an open source and free to use, distribute, and share; it is available at . Copyright © 2013 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Abstract: Markush structures are a special representation of the chemical compounds covered in patent documents. Due to their highly generic nature they are more difficult to index and search than specific chemical structures since they require special indexing and search features to make them searchable. Only a few databases exist that offer such features. The currently available indexing systems have been developed mainly in the 1960s to the 1980s, have not been majorly enhanced since then and their future seems somewhat uncertain. However, due to the fact that such Markush systems index unique information describing the chemistry protected by patent claims they are a necessary and indispensable information source for patent information professionals in the chemical industry in order to be able to support important business processes in chemical companies. Therefore we at BASF see a clear need to keep providing and also to keep developing such systems in the future. [Copyright &y& Elsevier]

The MOGADOC database (Molecular Gasphase Documenation) is a powerful tool to retrieve information about compounds which have been studied in the gas phase by means of electron diffraction, microwave spectroscopy or radio astronomy. Presently the database contains over 29,300 bibliographic references (from the inception of each method) for about 8700 inorganic, organic and organometallic compounds including numerical datasets for bond lengths and angles for about 5100 compounds. Two-dimensional and three-dimensional retrievals (searching of structural formulas and their fragments and the numeric searching of bond lengths and bond angles, respectively) are described. [Copyright &y& Elsevier]

The pressure-composition phase diagram of the W–Te system is constructed by ploting the convex hull. With the pressure increasing, stable WTe is discovered with a cubic crystal structure and WTe 2 decomposes into Te and WTe. The Cmcm phase of WTe 3 is successfully predicted at about 6 GPa and has critical superconducting temperature 3 K at 10 GPa. In the pressure range of 0–100 GPa, W 2 Te and W 3 Te can't be synthetized according to their formation enthalpy. Novel structural phase and superconductivity of W–Te compounds have been investigated using the developed particle swarm optimization algorithm in combination with ab initio calculations. Under ambient conditions, WTe 2 with Td phase is the most stable. with the pressure increasing, the 2H phase becomes stable until 60 GPa, and then WTe 2 decompose into Te and WTe with the Pm 3 m phase. More interesting, the layered Cmcm phase of WTe 3 is obtained at about 6 GPa, which remains stable up to 100 GPa. Moreover, electron–phonon calculations have been performed, which suggest that the Cmcm phase of WTe 3 is superconducting and the critical superconducting temperature can reach about 3 K at 10 GPa. [ABSTRACT FROM AUTHOR]

Various possible structures of ternary mononitrides of group 5 transition metals (V 0.5 Ta 0.5 N, V 0.5 Nb 0.5 N and Nb 0.5 Ta 0.5 N) are systematically explored in 0–300 GPa pressure range through CALYPSO (Crystal structure AnaLYsis by Particle Swarm Optimization) method. Three possible phases with Pmm 2, Cmc 2 1 , and Fm -3 m space group have been uncovered. Their dynamical, mechanical and thermodynamic stabilities are checked through calculations of phonon spectra, elastic constants and formation enthalpy. The elastic anisotropies are fully investigated by the dependence of linear bulk, Young's and shear moduli on the crystal orientations. To study the strength of these three compounds, the compressive, tensile and indentation shear strengths are systematically studied from the first-principles calculations. The mononitrides with Pmm 2 and Cmc 2 1 structures exhibit much better mechanical property relative to VN, NbN and TaN with traditional B1 (NaCl-like) structure. Our results reveal that the Pmm 2 and Cmc 2 1 phases of these three compounds possess the strength values up to 30 GPa under the Vickers indentation simulation calculations, which are comparable to well-known WB 3 , WB 4 and ReB 2 reported as potential superhard transition metal borides. Additionally, the electronic structures of these mononitrides are also studied to explore the intrinsic chemical bonding nature, and a novel transition of semiconductor-to-conductor from V 0.5 Ta 0.5 N, V 0.5 Nb 0.5 N to Nb 0.5 Ta 0.5 N is exposed for the Fm -3 m phases of these compounds. • Three new structures of V 0.5 Ta 0.5 N, V 0.5 Nb 0.5 N and Nb 0.5 Ta 0.5 N have been uncovered. • The theoretical hardness and ideal strength of V 0.5 Ta 0.5 N with Pmm 2 and Cmc 2 1 structures are predicted to be above 30 GPa. • The origin of the high hardness and high strength is the covalent bonding nature between TM and N atoms. [ABSTRACT FROM AUTHOR]

This communication summarizes the important points made in each contribution. They show that there remain issues in the cheminformatic handling of tautomers and predicting the relative energies of various tautomers. [ABSTRACT FROM AUTHOR]

The article offers information on the early days of the development of CAS (Chemical Abstract System) ONLINE which was released in December 1980. The structure searching principle was first introduced in the 1960s but was developed in the 1970s. CAS ONLINE was only searchable through screen numbers in its inception in the 1980s, then gained drawing query structure in 1981 through HP2647 terminal. It notes that in 1983, abstracts-containing bibliographic file were added in the structure.