Crystal structures and elastic properties of superhard IrN2 and IrN3 from first principles

First principles calculations were performed to investigate the structural, elastic, and electronic properties of IrN2 for various space groups: cubic Fm-3m and Pa-3, hexagonal P3(2)21, tetragonal P4(2)/mnm, orthorhombic Pmmn, Pnnm, and Pnn2, and monoclinic P2(1)/c. Our calculation indicates that the P2(1)/c phase with arsenopyrite-type structure is energetically more stable than the other phases. It is semiconducting (the remaining phases are metallic) and contains diatomic N-N with the bond distance of 1.414 A. These characters are consistent with the experimental facts that IrN2 is in lower symmetry and nonmetallic. Our conclusion is also in agreement with the recent theoretical studies that the most stable phase of IrN2 is monoclinic P2(1)/c. The calculated bulk modulus of 373 GPa is also the highest among the considered space groups. It matches the recent theoretical values of 357 GPa within 4.3% and of 402 GPa within 7.8%, but smaller than the experimental value of 428 GPa by 14.7%. Chemical bonding and potential displacive phase transitions are discussed for IrN2. For IrN3, cubic skutterudite structure (Im-3) was assumed.

Structures and elastic properties of OsN2 investigated via first-principles density functional calculations

The structure, elastic, and electronic properties of OsN2 at various space groups: cubic Fm-3m, Pa-3, and orthorhombic Pnnm were studied by first-principles calculations based on density functional theory. Our calculation indicates that the structure in orthorhombic Pnnm phase is energetically more stable compared with cubic systems. It is metallic, mechanically stable and contains diatomic N-N units with the bond distance 1.418 A. These characters are consistent with experimental facts that OsN2 is orthorhombic and metallic. The calculated bulk modulus 394 GPa is also the highest among the considered space groups, slightly larger than previous value 358 GPa. The calculated elastic anisotropic factors and directional bulk modulus showed that OsN2 possess high elastic anisotropy.

Hydrothermal synthesis of Fe and Mn doped SnO2 and its magnetic structures

The dilute magnetic semiconductor of Sn1-x-yMnxFeyO2 (0 <= x <= 0.10, 0 <= y <= 0.10) Were syhthesized with the hydrothermal method using SnCl4, Mn(CH3COO)(2) center dot 4H(2)O and FeCl3 center dot 6H(2)O as the raw materials. The structure, morphologies and magnetic properties of the sample were characterized via X-ray powder diffractometer(XRD), transmission electron microscopy(TEM), Raman spectrum and superconducting and quantum interference device(SQUIT), and Mossbeaur spectrum. No secondary phase was found in the XRD spectrum. The morphology of the samples is affected by the kind or the mount of transition metal. The local vibrating model-of Mn Positioned SnO2 sites was found in Raman spectrum. The measured magnetic results indicate that when x = 0.10, y = 0, the sample exhibits strong magnetization in low-temperature (5 K), but the magnetization decrease rapidly at room. temperature; In contrast, when x = 0, y = 0.1, the sample's magnetization and coercivity are both small, but being temperature independent. Mossbeaur spectra indicates that part of the Fe is ferromagnetic coupled, and the simulating results indicate that the ferromagnetic character is intrinsic.

Geometries and electronic properties of Ta-n, TanO and TaOn (n=1-3) clusters

Geometries, vibrational frequencies, electron affinities, ionization potentials and dissociation energies of the title clusters in both neutral and positively and negatively charged states were studied by use of density functional theory. For both neutral and charged species, different initial isomers were studied in order to determine the structure with the lowest energy. Vibrational analysis was also performed in order to characterize these isomers. For Ta-2, Ta-Ta metallic bond is strengthened by adding or removing an electron, i.e. the charged species are much more stable than the neutral counterpart. For Ta-3, equilateral triangle with D-3h symmetry has the lowest energy for both neutral and charged species (near equilateral triangle for cation). TaO and its charged species have much larger dissociation energy compared with other tantalum oxides. For Ta2O and TaO2. structure with C-2v symmetry is much more stable than linear chains. For Ta3O, planar structure with doubly bridging oxygen atoms of C-2v, symmetry is the global minimum for both neutral and charged species. While for TaO3, three-dimensional structures are favored for both neutral (C-1 symmetry) and charged species (C-3v symmetry).

Substitution effect of nitrogen atoms with carbon atoms in porphyrin on the electronic structure and excited states properties

Density functional theory (DFT) electronic structure calculations were carried out to predict the structures and the absorption and emission spectra for porphyrin and a series of carbaporphyrins-carbaporphyrin, adj-dicarbaporphyrin, opp-dicarbaporphyrin, tricarbaporphyrin and tetracarbaporphyrin. The ground- and excited-state geometries were optimized at the B3LYP/6-31g(d) and CIS/6-31g(d) level, respectively. The optimized ground-state geometry and absorption spectra of porphyrin, calculated by DFT and time-dependent DFT (TDDFT), are comparable with the available experimental values. Based on the optimized excited-state geometries obtained by CIS/6-31g(d) method, the emission properties are calculated using TDDFT method at the B3LYP/6-31g(d) level. The effects of the substitution of nitrogen atoms with carbon atoms at the center positions of porphyrin are discussed. The results indicate that the two-pyrrole nitrogens are important to the chemical and physical properties for porphyrin.

Morphology and structures of self-assembled symmetric poly(di-n-alkylsilanes)

The self-assembly of poly(di-n-butylsilane) (PDBS) and poly(di-n-hexylsilane) (PDHS) on the surfaces of amorphous carbon and highly oriented pyrolytic graphite (HOPG) have been investigated, respectively. The morphology and structures of these self-assembled thin films were studied by using atomic force microscopy, transmission electronic microscopy, and wide-angle X-ray diffraction. In the case of weak van der Waals interactions between absorbed molecules and substrate, i.e., on amorphous carbon, the self-assembly process was driven by absorbate-absorbate intermolecular interactions. For PDBS with weak absorbate-absorbate intermolecular interactions, the thin film showed organization lacking any measurable preferred orientation on the surface of amorphous carbon. While for PDHS with rigid backbone and strong intermolecular interactions, flat-on lamellae with silicon backbones perpendicular to the surface of amorphous carbon were formed. However, in the case of strong van der Waals interactions between absorbed molecules and substrate, i.e., on HOPG, the self-assembly process was tailored by the balance of absorbate-absorbate intermolecular interactions and molecule-substrate interactions. Both PDHS and PDBS thin films grew into edge-on lamellae on the surface of HOPG, which aligned according to a Mold symmetry.

Local structure and valences of samariurn in SrB4O7 : Sm and SrB6O10 : Sm prepared in-air

The coordination numbers for the samarium atoms and the Sm-O bond distances in SrB4O7:Sm and SrB6O10:Sm prepared in air were determined by means of Sm-L-3 edge EXAFS. The coordination. was found to be nine-folded for both these hosts and the bond distance was 2.40-2.42 Angstrom in SrB4O7:Sm and 2.42-2.44 Angstrom in SrB6O10:Sm. For SrB4O7:Sm the coordination number is coincident with that of the strontium. atoms suggesting the substitution of the samarium atoms at the strontium sites. The coordination number of the strontium atoms in SrB6O10 was also suggested to be nine assuming the same type of substitution. The valences of samarium were determined from the luminescent spectra. Both divalent and trivalent ions were present in both SrB4O7:Sm and SrB6O10:Sm, while the fraction of Sm2+ was higher in the former than in the latter. This difference has been assigned to the difference in rigidity between the B-O networks in these structures.

Investigation on moleculare and crystal structures of metal complexes with aminopolycarboxylic acids (VII) - Syntheses and structure determination of Na-3[Hg (I) (edta) C1] center dot 6H(2)O

In this paper we describe the moleculare and crystal structures of the Na-3[Hg( II )(edta)Cl] . 6H(2)O (edta=ethylenediamine-N,N,N',N'-tetraacetate). The crystal data are as follows: orthorhombic, a=8. 083 (2) Angstrom , b=13. 870(3) Angstrom , c=38. 617(5) Angstrom , v=4329. 4 (13) Angstrom(3) , Z=8, Dc= 1. 798 g . cm(-3), mu=5. 564 mm(-1), P(000)=2280, R=0. 0317 and R-w=0. 0731 for 3883 unique reflections. In complex, the complex anion [Hg ( II ) (edta)Cl](3-) has a seven-coordination structure like a mono-capped trigonal-prism (C-2v-MTP) in which the edta(4-) acts as a hexadentate ligand with four O atoms and two N atoms and a Cl- caps a quadrilateral face as a seventh ligand. It can be known that the Hg2+ which has a d(10) electronic structure can form a high-coordinate compound with a hexadentate ligand (edta) because it has a big ionic radius.

Local similarity in organic crystals and the non-uniqueness of X-ray powder patterns

Two new concepts for molecular solids, 'local similarity' and 'boundary-preserving isometry', are defined mathematically and a theorem which relates these concepts is formulated. 'Locally similar' solids possess an identical short-range structure and a 'boundary-preserving isometry' is a new mathematical operation on a finite region of a solid that transforms mathematically a given solid to a locally similar one. It is shown further that the existence of such a 'boundary-preserving isometry' in a given solid has infinitely many 'locally similar' solids as a consequence. Chemical implications, referring to the similarity of X-ray powder patterns and patent registration, are discussed as well. These theoretical concepts, which are first introduced in a schematic manner, are proved to exist in nature by the elucidation of the crystal structure of some diketopyrrolopyrrole (DPP) derivatives with surprisingly similar powder patterns. Although the available powder patterns were not indexable, the underlying crystals could be elucidated by using the new technique of ab initio prediction of possible polymorphs and a subsequent Rietveld refinement. Further ab initio packing calculations on other molecules reveal that 'local crystal similarity' is not restricted to DPP derivatives and should also be exhibited by other molecules such as quinacridones. The 'boundary-preserving isometry' is presented as a predictive tool for crystal engineering purposes and attempts to detect it in crystals of the Cambridge Structural Database (CSD) are reported.

Structures and vibrational spectra of C-2 and LaC2+ clusters

C-2 and LaC2+ were studied using Hartree-Fock(HF), B3LYP (Becke 3-paremeter-Lee-Yang-Parr) density functional method, second-order Moller-Plesset perturbation (MP2) and coupled cluster singles and doubles with non-iterative triples(CCSD(T)) methods. The basis set employed was LANL1DZ. Geometries, vibrational frequencies and other quantities were reported. The results showed that for C-2, all the methods performed well for low spin state (singlet), while only HF and B3LYP remained so for high spin state (triplet). For LaC2+, four isomers were presented and fully optimized. The results suggested that linear isomers with C-infinity v and D-infinity h symmetries were predicted to be saddle points on the energy surface for all the methods, while for isomers with C-2 upsilon and C-s symmetries, they were local minima except C-2 upsilon at B3LYP level, and were isoenergetic at HF, MP2 and CCSD(T) levels, near isoenergetic at B3LYP level. From the differences between HOMO and LUMO, it is also known that the isomers with C-2 upsilon and C-s symmetries offer the largest values and therefore correspond to the most stable structure. For La-C bond lengths, B3LYP gives the shortest, the order is B3LYP

Studies on the energy band structures and chemical bond properties of LaX(X=N, P, As, Sb) crystals

The energy band structures of LaX(X=N, P, As, Sb) crystals have been studied by using LMTO-ASA method. The calculated energy gaps of these crystals are 2. 30 eV for LaN, 2. 05 eV for LaP, 1. 66 eV for LaAs and 1. 34 eV for LaSb. The results are in good agreement with experimental data, At the same time, using these calculated results of energy band structures of these crystals, the chemical bond properties have been analyzed and calculated, The covalency values of these crystals are 26.15% for LaN, 32.54% for LaP, 33.30% for LaAs and 36.49% for LaSb, which agree satisfactorily with the calculated ones by using PV (Phillips-Vechten) theory.

Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.