Preparation of niobium based oxynitride nanosheets by exfoliation of Ruddlesden-Popper phase precursor

A new oxynitride Ruddlesden-Popper phase K_1.6Ca₂Nb₃O_9.4N_0.6.1.1H₂O was synthesized by the topochemical ammonolysis reaction at 700 °C from the oxide Dion-Jacobson phase KCa₂Nb₃O₁₀ in the presence of K₂CO₃. The oxynitride showed good stability with a little loss of nitrogen, even after a few months of exposure to air. Its crystal structure was solved by Rietveld refinement of X-ray powder diffraction data in space group P4/mmm and considering a two-phase mixture, due to the difference in the degree of hydration, with a = 3.894(2) Å and c = 17.90(8) Å for the most hydrated phase and a = 3.927(6) Å and c = 17.09(2) Å for the less one. Optical band gaps were measured by diffuse reflectance in the UV-Visible range indicating a red shift of Eg to the visible region. The oxynitride layered perovskite was then protonated and exfoliated into nanosheets. TEM images and SAED patterns of the nanosheets proved that exfoliation was successful, showing lattice parameters quite compatible with the Rietveld refinement.     

Characterizing the constitutive response and energy absorption of rigid polymeric foams subjected to intermediate-velocity impact

As an optimum energy-absorbing material system, polymeric foams are needed to dissipate the kinetic energy of an impact, while maintaining the impact force transferred to the protected object at a low level. Therefore, it is crucial to accurately characterize the load bearing and energy dissipation performance of foams at high strain rate loading conditions. There are certain challenges faced in the accurate measurement of the deformation response of foams due to their low mechanical impedance. In the present work, a non-parametric method is successfully implemented to enable the accurate assessment of the compressive constitutive response of rigid polymeric foams subjected to impact loading conditions. The method is based on stereovision high speed photography in conjunction with 3D digital image correlation, and allows for accurate evaluation of inertia stresses developed within the specimen during deformation time. Full-field distributions of stress, strain and strain rate are used to extract the local constitutive response of the material at any given location along the specimen axis. In addition, the effective energy absorbed by the material is calculated. Finally, results obtained from the proposed non-parametric analysis are compared with data obtained from conventional test procedures.     

Cluster analysis of molecular simulation trajectories for systems where both conformation and orientation of the sampled states are important

Clustering methods have been widely used to group together similar conformational states from molecular simulations of biomolecules in solution. For applications such as the interaction of a protein with a surface, the orientation of the protein relative to the surface is also an important clustering parameter because of its potential effect on adsorbed‐state bioactivity. This study presents cluster analysis methods that are specifically designed for systems where both molecular orientation and conformation are important, and the methods are demonstrated using test cases of adsorbed proteins for validation. Additionally, because cluster analysis can be a very subjective process, an objective procedure for identifying both the optimal number of clusters and the best clustering algorithm to be applied to analyze a given dataset is presented. The method is demonstrated for several agglomerative hierarchical clustering algorithms used in conjunction with three cluster validation techniques. © 2016 Wiley Periodicals, Inc.     

Electrostatic component of binding energy: Interpreting predictions from poisson–boltzmann equation and modeling protocols

Macromolecular interactions are essential for understanding numerous biological processes and are typically characterized by the binding free energy. Important component of the binding free energy is the electrostatics, which is frequently modeled via the solutions of the Poisson–Boltzmann Equations (PBE). However, numerous works have shown that the electrostatic component (ΔΔG_elec) of binding free energy is very sensitive to the parameters used and modeling protocol. This prompted some researchers to question the robustness of PBE in predicting ΔΔG_elec. We argue that the sensitivity of the absolute ΔΔG_elec calculated with PBE using different input parameters and definitions does not indicate PBE deficiency, rather this is what should be expected. We show how the apparent sensitivity should be interpreted in terms of the underlying changes in several numerous and physical parameters. We demonstrate that PBE approach is robust within each considered force field (CHARMM‐27, AMBER‐94, and OPLS‐AA) once the corresponding structures are energy minimized. This observation holds despite of using two different molecular surface definitions, pointing again that PBE delivers consistent results within particular force field. The fact that PBE delivered ΔΔG_elec values may differ if calculated with different modeling protocols is not a deficiency of PBE, but natural results of the differences of the force field parameters and potential functions for energy minimization. In addition, while the absolute ΔΔG_elec values calculated with different force field differ, their ordering remains practically the same allowing for consistent ranking despite of the force field used. © 2016 Wiley Periodicals, Inc.     

Perceptron ensemble of graph-based positive-unlabeled learning for disease gene identification

Identification of disease genes, using computational methods, is an important issue in biomedical and bioinformatics research. According to observations that diseases with the same or similar phenotype have the same biological characteristics, researchers have tried to identify genes by using machine learning tools. In recent attempts, some semi-supervised learning methods, called positive-unlabeled learning, is used for disease gene identification. In this paper, we present a Perceptron ensemble of graph-based positive-unlabeled learning (PEGPUL) on three types of biological attributes: gene ontologies, protein domains and protein-protein interaction networks. In our method, a reliable set of positive and negative genes are extracted using co-training schema. Then, the similarity graph of genes is built using metric learning by concentrating on multi-rank-walk method to perform inference from labeled genes. At last, a Perceptron ensemble is learned from three weighted classifiers: multilevel support vector machine, k-nearest neighbor and decision tree. The main contributions of this paper are: (i) incorporating the statistical properties of gene data through choosing proper metrics, (ii) statistical evaluation of biological features, and (iii) noise robustness characteristic of PEGPUL via using multilevel schema. In order to assess PEGPUL, we have applied it on 12950 disease genes with 949 positive genes from six class of diseases and 12001 unlabeled genes. Compared with some popular disease gene identification methods, the experimental results show that PEGPUL has reasonable performance.     

Two concomitant polymorphs of 3,3′,4,4′-tetrakis(phenylethynyl)-1,1′-[2,2,2,-trifluoro- 1-(trifluromethyl)ethanediyl]bisbenzene

A representative compound of bis-ortho-diynyl arene (BODA), with a general formula [(m,p)R₂–Ph]₂ –X, where R: –C≡C–Ph and X: >C(CF₃)₂ has been structurally characterized. The compound is being investigated as a monomer for high-performance polyarylene networks and glassy carbon precursors. The bis(trifluoromethyl) derivative crystallizes in two concomitant polymorphic forms. The two polymorphs form a monotropic system with melting points of 436 and 463 K. The metastable form yields monoclinic crystals (P2₁/n, Z=4). a=12.677(3) ?, b=11.677(2) ?, c=24.026(5) ?, β=93.79(3)°. The thermodynamically stable form is monoclinic as well (P2₁/c, Z=8), a=10.7983(6) ?, b=30.628(2) ?, c=21.648(1) ?, β=94.737(1)° with small voids indicating less efficient packing. The two polymorphs contain different conformers of the rotationally flexible molecule.     

6<Emphasis Type="Italic">S</Emphasis>,8α-Dihydroxy-14,15-Dihydrocarapin (Khayanone) from the Stem Bark of <Emphasis Type="Italic">Khaya Senegalensis</Emphasis> (Meliaceae): Isolation and its Crystal Structure

Khayanone was isolated from the stem bark of African mahogany, Khaya senegalensis (Meliaceae), and characterized as 6S,8α-dihydroxy-14,15-dihydrocarapin on the basis of spectral analysis and single crystal X-ray diffraction study. The compound crystallizes in the tetragonal space group P4 ₁ 2 ₁ 2 with unit cell parameters: a = 13.2315(19) Å, c = 29.118(6) Å, Z = 8. The crystal structure has been solved by direct methods and refined to R = 0.0375 for 4552 unique reflections. The six-membered rings A and B exist in boat conformations, rings C and D in chair conformations, and the furan ring is planar. The crystal structure is stabilized by O-H···O and C-H···O interactions. This is the first report about 6S configuration of mexicanolide revealed by X-ray diffraction analysis. The configuration of oxygenated C-6 in mexicanolide-group limonoids is discussed.     

Synthesis and characterization of MAgSe4 (M=Rb, Cs)

Syntheses of the title compounds were achieved from supercritical amines. The single crystal X-ray characterization of both MAgSe₄ (M=Rb, Cs) members indicates that they are isostructural. The structure is built from five membered AgSe₄ rings that are stitched together through tetrahedrally coordinated Ag(I) ions to form one dimensional chains running parallel to the a-axis. These chains are separated from each other by the alkali metal cations. Crystal data: orthorhombic, P2₁2₁2₁, Z = 4. RbAgSe₄: a = 5.809(2), b = 8.927(3), c = 13.435(4) Å, U = 698.2(4) ų, and D _c = 4.851 g/cm³. CsAgSe₄: a = 5.855(2), b = 9.090(3), c = 13.885(4) Å, U = 739.0(4) ų, and D _c = 5.003 g/cm³. The anionic chain found in the title compounds has been observed previously, and comparisons among these phases show that the silver ion coordination in the chain varies as a function of cation size. Both the title compounds are valence precise and optical diffuse reflectance studies show that they are semiconductors with moderately large band gaps.     

Tricarbonyl (η6 arene) chromium(0) complex derived from 8-phenylmenthol chiral auxiliary

(—)-8-Phenylmenthol was prepared and converted to the corresponding tricarbonyl (⁶-arene) chromium(0) complex. Derivitization as the acrylate ester (1) and subsequent X-ray analysis revealed a 1:1 mix of s-cis and s-trans acrylate in the unit cell, and geometric proximity to support a through-space stacking interaction in the case of the s-trans isomer. The dihedral angle between the best planes through the chromium-bound aryl ring and the acrylate group is 19.9° for the s-trans isomer and 34.4° for the s-cis isomer. Crystal data for (1): C₂₂H₂₆O₅Cr, monoclinic, P2₁ (No. 4), a = 10.269(1), b = 10.482(1), c = 19.787(2), = 95.85(1), Z = 4, and D _calc = 1.32 g cm^–3.     

Crystal and molecular structure of chlorotris(monomethylthiourea)silver(I)

The crystal and molecular structure of chlorotris(monomethylthiourea)silver(I) has been solved and refined by full-matrix least-squares methods to a finalR of 0·039 from 1150 reflections measured by counter techniques at ambient room temperature. The crystals are orthorhombic:Pmcn, a = 14·824(2),b = 8·524(1),c = 12·671(1) Å,Z = 4,D _m = 1·68,D _c = 1·72 gcm^–3. The structure consists of independent, distorted tetrahedral Ag(I) moieties with only weak hydrogen bonds and/or van der Waals interactions between molecules. These molecules are packed in such a way that Ag, Cl and one entire monomethylthiourea ligand all lie in a crystallographic mirror plane, and the other two ligands are related by this mirror. This arrangement, plus the alternation of the Ag-Cl bond direction, leads to a non-polar sheet of Ag, Cl and monomethylthiourea groups with other monomethylthiourea groups protruding from either side of the sheet. Only N-HCl hydrogen bonds and van der Waals interactions exist between sheets. The Ag-S distance is somewhat long at 2·649(3) Å, as is one of the Ag-S distances at 2·665(3) Å. The other two Ag-S distances are 2·520(2) Å. The geometry of the complex makes it clear that the Ag-S bond is formed by donation of an electron pair from a sulfur sp² orbital.