Retro–Leapfrog and structure elucidation

Operations on maps are topological-geometrical tools used for transforming a given polyhedral tessellation. Investigation of fullerene structure often needs information on the original map which transformed into a larger molecular structure. Operations leading to the previous, smaller structures are called Retro-operations. They appear particularly useful in studies of structure elucidation or stability of series of fullerenes. The paper presents the first structure affiliation of the well-known C₆₀ fullerene to a family of Leapfrog fullerenes with relatedness being established by map operation. Thus, the tessellation of C₆₀ is described as an Archimedean, joint Sumanene-hexagon covering, in tetrahedral disposition. The other members of family show essentially the same covering and predicted good stability. Related Leapfrog fullerenes showing a disjoint Sumanene covering are also given.     

Crystal structure of natural Ag–Cu–Pb–Bi sulfide

The crystal structure of a natural sulfide Cu_3,44Ag_0,56Pb₂Bi₆S₁₃ (Сmcm, Z = 4, a = 3.973(1) Å, b = 13.370(2) Å, c = 42.182(7) Å, R = 0.059) is determined. The structure has seven cation positions: two of them (Cu and Ag) are in a tetrahedral environment of sulfur atoms; one (Pb), in a special position (mm2), has a coordination polyhedron in the form of a bicapped trigonal prism; and the other cation positions are surrounded by sulfur atoms forming distorted octahedra. The mirror symmetry plane perpendicular to the c translation causes microtwinning by cutting a layer of trigonal prisms framed by tetrahedron ribbons. These layers are divided by those composed by edge-linked octahedra with a diagonal ribbon of five octahedra (N = 5). The cation and anion positions are ordered by individual sublattices with pseudohexagonal subcells on the m planes perpendicular to the a translation, which concentrate the positions of all the atoms. Supposedly, this natural sulfide is the previously described (1885) yet unconfirmed alaskaite mineral from the lillianite–heyrovskyite homological series and may be isostructural to the ourayite mineral.     

Small-scale structure in fluid cholesterol–lipid bilayers

Cholesterol is the single most abundant molecule in animal plasma membranes, in the range of 20–30 mol%, where it is known to modulate the lipid-bilayer component of the membrane and lead to increased mechanical stability, lower permeability, larger thickness, and a distinct lateral organization. The phase equilibria of membranes with cholesterol and the associated large- and small-scale structure have turned out to be a particularly elusive problem. With the proposal that lipid domains and so-called ‘rafts’, characterized by high local levels of cholesterol in a liquid-ordered phase, are important for a wide range of cellular functions, an understanding and a quantitative assessment of the nature of these cholesterol-induced structures and their types of ordering have become urgent. Recent progress in neutron diffraction studies of lipid–cholesterol model membranes has now revealed details of the lateral ordering, and combined with earlier molecular model studies a picture emerges of the membrane as a locally structured liquid with small ordered ‘domains’ of a highly dynamic nature.     

Synthesis–structure correlations of manganese–cobalt mixed metal oxide nanoparticles

Mixed metal oxides in the nanoscale are of great interest for many aspects of energy related research topics as water splitting, fuel cells and battery technology. The development of scalable, cost-efficient and robust synthetic routes toward well-defined solid state structures is a major objective in this field.While monometallic oxides have been studied in much detail, reliable synthetic recipes targeting specific crystal structures of mixed metal oxide nanoparticles are largely missing. Yet, in order to meet the requirements for a broad range of technical implementation it is necessary to tailor the properties of mixed metal oxides to the particular purpose. Here, we present a study on the impact of the nature of the gas environment on the resulting crystal structure during a post-synthesis thermal heat treatment of manganese–cobalt oxide nanoparticles. We monitor the evolution of the crystal phase structure as the gas atmosphere is altered from pure nitrogen to synthetic air and pure oxygen. The particle size and homogeneity of the resulting nanoparticles increase with oxygen content, while the crystal structure gradually changes from rocksalt-like to pure spinel. We find the composition of the particles to be independent of the gas atmosphere. The manganese–cobalt oxide nanoparticles exhibited promising electrocatalytic activity regarding oxygen evolution in alkaline electrolyte. These findings offer new synthesis pathways for the direct preparation of versatile utilizable mixed metal oxides.     

Thermoanalytical study and structure of stoichiometric As–Sb–S glasses

The glass-forming system (As₂S₃)_100?x(Sb₂S₃)_x was studied by thermal analysis (conventional and StepScan differential scanning calorimetry) and Raman spectroscopy. It was found that the bulk glasses are homogeneous up to x = 60, while supercooled melts are unstable and when x ≥ 40, Sb₂S₃ (stibnite) crystallizes during heating. Depending on the chemical composition, the glass transition temperature initially increases as the Sb₂S₃ concentration is increased from 0 to 5 %, decreases to a minimum at ~20 %, and then gradually increases as the concentration is further increased and the main Raman peak also shifts non-monotonically. Combining these results with chemometric analysis of the Raman spectra showed that the image of the structure of the studied glasses can be described by the linear combination of three chemically different stable clusters, rather than by the chains crossing model, CCM, and that the properties of the glasses are controlled by medium-range order.     

Thermodynamics,structure and kinetics in the system Ga–O–N

Within the ternary system Ga–O–N we performed experimental and theoretical investigations on the thermodynamics, structure and kinetics of new stable and metastable compounds.We studied the ammonolysis of β-Ga₂O₃ at elevated temperatures by means of ex situ X-ray diffraction, ex situ neutron diffraction, and in situ X-ray absorption spectroscopy (XAS). From total diffraction pattern refinement with the Rietveld method we analyzed the anionic occupancy factors and the lattice parameters of β-Ga₂O₃ during the reaction. Within the detection limits of these methods, we can rule out the existence of a crystalline oxynitride phase that is not derived from wurtzite-type GaN. The nitrogen solubility in β-Ga₂O₃ was found to be below the detection limit of about 2–3 at.% in the anionic sublattice. The kinetics of the ammonolysis of β-Ga₂O₃ to α-GaN and of the oxidation of α-GaN to β-Ga₂O₃ was studied by means of in situ X-ray absorption spectroscopy. In both cases the reaction kinetics could be described well by fitting linear combinations of β-Ga₂O₃ and α-GaN spectra only, excluding that other crystalline or amorphous phases appear during these reactions. The kinetics of the ammonolysis can be described well by an extended Johnson–Mehl–Avrami–Kolmogorow model with nucleation and growth of GaN nuclei, while the oxidation kinetics can be modeled by a shrinking core model where Ga₂O₃ grows as a layer. Investigations by means of TEM and SEM support the assumptions in both models.To investigate the structure and energetics of spinel-type gallium oxynitrides (γ-galons) we performed first-principles calculations using density-functional theory. In addition to the ideal cubic γ-Ga₃O₃N we studied gallium deficient γ-galons within the Constant-Anion-Model.In highly non-stoichiometric, amorphous gallium oxide of approximate composition GaO_1.2 we found at a temperature around 670 K an insulator–metal transition, with a conductivity jump of seven orders of magnitude. We demonstrate through experimental studies and density-functional theory calculations that the conductivity jump takes place at a critical gallium concentration and is induced by crystallization of stoichiometric β-Ga₂O₃ within the metastable oxide matrix. By doping with nitrogen the critical temperature and the conductivity in the highly conducting state can be tuned.     

Local structure of ionic liquid–monohydric alcohol solutions

The method of molecular dynamics is used to investigate the effect of monohydric alcohols on the formation of the local structure of ionic liquids based on the dimethylimidazolium cation at T = 400 K. The intermolecular interaction energies are analyzed to find that the increase in the length of the alkyl chain in the alcohol molecule reduces the influence of the solute molecule on the formation of the local structure of the dmim⁺/Cl^––solute molecule systems. An analysis of the radial distribution function shows that the change in the structure and physical characteristics of the solute molecule does not affect the interaction between the hydroxyl group proton of the alcohol molecule and the ionic liquid anions, whose interactions form the hydrogen bond H^alcohol…Cl^– with a length of 2.3 Å.     

Representation of molecular structure using quantum topology with inductive logic programming in structure–activity relationships

The requirement of aligning each individual molecule in a data set severely limits the type of molecules which can be analysed with traditional structure activity relationship (SAR) methods. A method which solves this problem by using relations between objects is inductive logic programming (ILP). Another advantage of this methodology is its ability to include background knowledge as 1st-order logic. However, previous molecular ILP representations have not been effective in describing the electronic structure of molecules. We present a more unified and comprehensive representation based on Richard Bader's quantum topological atoms in molecules (AIM) theory where critical points in the electron density are connected through a network. AIM theory provides a wealth of chemical information about individual atoms and their bond connections enabling a more flexible and chemically relevant representation. To obtain even more relevant rules with higher coverage, we apply manual postprocessing and interpretation of ILP rules. We have tested the usefulness of the new representation in SAR modelling on classifying compounds of low/high mutagenicity and on a set of factor Xa inhibitors of high and low affinity.     

Molecular–topological structure of tetrafluoroethylene–perfluoromethylvinyl ether copolymer irradiated with MeV protons

The molecular–topological structure of a copolymer of tetrafluoroethylene and perfluoromethylvinyl ether has been studied for the first time before and after irradiation with 1- and 4-MeV protons. The pseudo-network structure of the copolymer contains an amorphous block and crystalline segments of macromolecules as branching points. After bombardment with protons, a high-temperature amorphous block is formed in the copolymer with simultaneous complete amorphization of the copolymer structure and a decrease in its molecular flow temperature. The surface of a target plate with a thickness of 500 μm that has not been directly exposed to proton bombardment preserves the molecular–topological structure of the initial copolymer.     

Protein–protein interface prediction based on hexagon structure similarity

Studies on protein–protein interaction are important in proteome research. How to build more effective models based on sequence information, structure information and physicochemical characteristics, is the key technology in protein–protein interface prediction. In this paper, we study the protein–protein interface prediction problem. We propose a novel method for identifying residues on interfaces from an input protein with both sequence and 3D structure information, based on hexagon structure similarity. Experiments show that our method achieves better results than some state-of-the-art methods for identifying protein–protein interface. Comparing to existing methods, our approach improves F-measure value by at least 0.03. On a common dataset consisting of 41 complexes, our method has overall precision and recall values of 63% and 57%. On Benchmark v4.0, our method has overall precision and recall values of 55% and 56%. On CAPRI targets, our method has overall precision and recall values of 52% and 55%.     

Sol–gel synthesis and structure of silica hybrid materials

In this work the research results on the sol–gel synthesis and structure of silica nanocomposites, containing carrageenan and their application as carriers for cell immobilization were described. The samples were prepared at room temperature by replacing different quantity of the inorganic precursor with κ-carrageenan. For studying the structure of the synthesized hybrids the following methods were used: FT-IR, XRD, BET-Analysis, SEM, AFM and Roughness Analysis. The influence of the type of silicon precursors, nature and quantity of organic component on the structure, surface area, design and size of nanostructures was established. The possibility of application of the synthesized biocatalysts in an enzyme degradation process of the toxic, carcinogenic and mutagenic substances benzonitrile, fumaronitrile, o-, m-, and p-tolunitriles was investigated at batch experiments. A two-step biodegradation process in a column bioreactor of fumaronitrile was followed. After operation of the system for 8 h at a flow rate 45 mL h^?1 and at 60 °C, the overall conversion was 89%, showing a good stability of the developed process.     

Strong cellulose nanofibre–nanosilica composites with controllable pore structure

Flexible nanocellulose composites with silica nanoparticle loading from 5 to 77 wt% and tunable pore size were made and characterised. The pore structure of the new composites can be controlled (100–1000 nm to 10–60 nm) by adjusting the silica nanoparticle content. Composites were prepared by first complexing nanoparticles with a cationic dimethylaminoethyl methacrylate polyacrylamide, followed by retaining this complex in a nanocellulose fibre network. High retention of nanoparticles resulted. The structural changes and pore size distribution of the composites were characterised through scanning electron microscopy (SEM) and mercury porosimetry analysis, respectively. The heavily loaded composites formed packed bed structures of nanoparticles. Film thickness was approximately constant for composites with low loading, indicating that nanoparticles filled gaps created by nanocellulose fibres without altering their structure. Film thickness increased drastically for high loading because of the new packed bed structure. Unexpectedly, within the investigated loading range, the level of the tensile index on nanocellulose mass basis remained constant, showing that the silica nanoparticles did not significantly interfere with the bonding between the cellulose nanofibres. This hierarchically engineered material remains flexible at all loadings, and its unique packing enables use in applications requiring nanocellulose composites with controlled pore structure and high surface area.     

Thermal properties and structure of zinc–manganese metaphosphate glasses

Journal of Thermal Analysis and Calorimetry - The thermal properties and some physical characteristics of the metaphosphate glassy system xMnO–(50?x)ZnO–50P2O5 were studied....     

Acid–base behavior of oxides and their electronic structure

We attempted to simplify and unify the former concepts describing the acid base character of oxides on the basis of their band structure. Duffy optical basicity, Smith acid scale and Bratsch electronegativity model can simply be linked by taking into account the electronegativity and the chemical hardness of the oxides: an acidic oxide has a strong electronegativity together with a strong chemical hardness while a basic oxide has a low electronegativity associated with a weak chemical hardness.     

Synthesis,structure and thermal properties of propylene oxide–carbon dioxide–L-lactide terpolymers

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Visual exploration of structure–activity relationship using maximum common framework

To help tracking all molecules made in a typical medicinal chemistry project, we have developed an algorithm to generate a maximum common framework (MCF) hierarchy and an interactive tool for its visualization and analysis. By identifying all unique frameworks for a set of molecules and all molecules containing each framework, we were able to simplify the MCF hierarchy build up steps and, as a result, speed up the entire process significantly. By allowing compounds to be assigned to multiple MCFs, users can easily remove bad branching nodes and concentrate on interesting ones. MCF hierarchies provide an effective and intuitive visualization for tracking medicinal chemistry lead optimization projects. We will provide examples to illustrate its usefulness.