Doping effects of B and N on hydrogen adsorption in single-walled carbon nanotubes through density functional calculations

The doping effects of B and N on atomic and molecular adsorption of hydrogen in single-walled carbon nanotubes (SWNTs) were investigated through density functional theory (DFT) calculations. The hydrogen adsorption energies and electronic structures were calculated for the pristine and B- or N-doped SWNTs. The B-doping increases the hydrogen atomic adsorption energies both in zigzag and armchair nanotubes. The B-doping forms an electron-deficient six-membered ring structure, and when hydrogen is adsorbed on top of B atom, a coordination-like B-H bond will form. The N-doping forms an electron-rich six-membered ring structure, and decreases the hydrogen atomic adsorption energies in the N-doped SWNT. In case of hydrogen molecular adsorption, both B- and N-doping decrease the adsorption energies in SWNTs.     

Investigation of the thin film crystallization of a DNA copolymer hybrid composed of chitosan

We describe for the first time the crystallization in thin films of a DNA copolymer composed of a low molecular weight chitosan backbone to which a sequence of nucleic acids is grafted (chitosan‐g‐ssDNA). As assessed by atomic force microscopy, optical microscopy and spectroscopy, crystallization occurs due to intermolecular hydrogen bonding in which the nucleic acid strands engage. The morphology of the crystals depends on the affinity for the surface of the polymer segments that compose the DNA copolymer hybrid. The nucleic acids adsorb on mica and silica on which side‐branched structures are observed whereas chitosan interacts preferentially with gold, and dendritic crystals are assembled. Attenuated total reflectance infrared spectroscopy supports the high ordering of the structure and the establishment of strong intermolecular interactions by hydrogen bonding. © 2016 Society of Chemical Industry     

密度泛函理论研究总姜黄素的结构和性质

采用量子化学软件Gaussian03在B3LYP/6-31+G(d)水平下使用密度泛函理论方法优化3种姜黄素的分子结构并计算频率。根据前沿分子轨道理论及原子净电荷等量化参数,分析了化合物的结构与活性关系。     

Dependence of Grain Growth and Grain-Boundary Structure on the Ba/Ti Ratio in BaTiO3

The grain-growth behavior and grain-boundary structure in titanium-excess BaTiO₃ depend on the amount of excess titanium at 1250° and 1300°3C. With excess titanium, abnormal grain growth (AGG) occurs and the grain boundaries are mostly flat or faceted with hill-and-valley shapes. With 0.5 at.% excess titanium, the large grains have flat {111} faces forming singular grain boundaries parallel to {111} double twins. With excess-titanium content between 0.1 and 0.3 at.%, the abnormal grains appear to have polyhedral shapes with {100} faces. These flat or faceted grain boundaries are expected to have singular structures, and hence AGG can occur by the step growth mechanism. When the excess-titanium content is decreased to 0, the grain boundaries become curved, indicating a rough atomic structure, and normal grain growth occurs.     

Atomic and micro-structure features of nanoporous aluminosilicate glasses from reactive molecular dynamics simulations

Long-term chemical durability of borosilicate glasses that makes them a widely accepted form of nuclear waste disposal is achieved through the formation of a porous aluminosilicate gel layer that provides passivity and limits the transport of water to the reaction front. Detailed understanding of the porous silicate gel layer is thus critical in elucidating the corrosion mechanism of these glasses and to design of new glass composition for waste immobilization and other applications. In this paper, we use the diffuse charge reactive potential to generate porous aluminosilicate glass structures with compositions equivalent to the gel layers formed at the glass-water interface with an aim to understand the processing condition on the microstructure and atomic structure of these systems. We demonstrate the use of the charge scaling techniques is an effective approach to generate these porous structures with controllable pore mophologies. After initial validation of the potentials and calcium aluminosilicate glass structures using neutron diffraction, we created gel structures with compositions similar to well-known model nuclear waste borosilicate glasses. The porosities and the pore size distribution bear a strong correlation to the processing temperature, as well as to the local atomic structure. Thus, by controlling the processing parameters, the generated porous structures can be customized to closely resemble gel structures due to borosilicate glass corrosion. These results provide insights of the micro- and atomic structure features of the porous aluminosilicate glasses and on the optimal procedure to generate porous structures that can be comparable to experimentally observed gel layer structures thus to elaborate on the correlations between the structure and phenomena in glass-water interactions.     

生物活性多糖高级结构的研究方法进展

不同化学结构的多糖具有不同的生物活性,研究多糖的结构是揭示其构效关系的基础。多糖的结构可分为一级结构和高级结构。本文综述X-射线衍射法（XRD）、毛细管电泳法（CE）、核磁共振法（NMR）、旋光度（ORD）和圆二色谱（CD）、快原子轰击质谱（FAB-MS）、气色质联用（GC-MS）、原子力显微镜（AFM）等检测手段在多糖高级结构分析中的应用研究进展。     

Atomistic modeling of crystal structure of Ca1.67SiHx

The atomic structure of calcium-silicate-hydrate (C_1.67-S-H_x) has been investigated by theoretical methods in order to establish a better insight into its structure. Three models for C-S-H all derived from tobermorite are proposed and a large number of structures were created within each model by making a random distribution of silica oligomers of different size within each structure. These structures were subjected to structural relaxation by geometry optimization and molecular dynamics steps. That resulted in a set of energies within each model. Despite an energy distribution between individual structures within each model, significant energy differences are observed between the three models. The C-S-H model related to the lowest energy is considered as the most probable. It turns out to be characterized by the distribution of dimeric and pentameric silicates and the absence of monomers. This model has mass density which is closest to the experimental one.     

Investigating the structural evolution of thiolate protected gold clusters from first-principles

Unlike bulk materials, the physicochemical properties of nano-sized metal clusters can be strongly dependent on their atomic structure and size. Over the past two decades, major progress has been made in both the synthesis and characterization of a special class of ligated metal nanoclusters, namely, the thiolate-protected gold clusters with size less than 2 nm. Nevertheless, the determination of the precise atomic structure of thiolate-protected gold clusters is still a grand challenge to both experimentalists and theorists. The lack of atomic structures for many thiolate-protected gold clusters has hampered our in-depth understanding of their physicochemical properties and size-dependent structural evolution. Recent breakthroughs in the determination of the atomic structure of two clusters, [Au(25)(SCH(2)CH(2)Ph)(18)](q) (q = -1, 0) and Au(102)(p-MBA)(44), from X-ray crystallography have uncovered many new characteristics regarding the gold-sulfur bonding as well as the atomic packing structure in gold thiolate nanoclusters. Knowledge obtained from the atomic structures of both thiolate-protected gold clusters allows researchers to examine a more general "inherent structure rule" underlying this special class of ligated gold nanoclusters. That is, a highly stable thiolate-protected gold cluster can be viewed as a combination of a highly symmetric Au core and several protecting gold-thiolate "staple motifs", as illustrated by a general structural formula [Au](a+a')[Au(SR)(2)](b)[Au(2)(SR)(3)](c)[Au(3)(SR)(4)](d)[Au(4)(SR)(5)](e) where a, a', b, c, d and e are integers that satisfy certain constraints. In this review article, we highlight recent progress in the theoretical exploration and prediction of the atomic structures of various thiolate-protected gold clusters based on the "divide-and-protect" concept in general and the "inherent structure rule" in particular. As two demonstration examples, we show that the theoretically predicted lowest-energy structures of Au(25)(SR)(8)(-) and Au(38)(SR)(24) (-R is the alkylthiolate group) have been fully confirmed by later experiments, lending credence to the "inherent structure rule".     

Matrix synthesis of water-soluble polyaniline in the presence of polyelectrolytes

The matrix polymerization of aniline hydrochloride in the presence of polyanions with different chemical structures and molecular masses is studied. Poly(2-acrylamido-2-methyl-1-propanesulfonic acid) and poly(4-styrenesulfonic acid) or its sodium salt are used as polyelectrolyte matrices. It is shown that, if the polymerization of aniline hydrochloride is conducted in the presence of a polyelectrolyte matrix, water-soluble polyelectrolyte complexes in which polyaniline occurs in the form of an emeraldine salt are formed. The mechanism of polymerization is advanced. It is found that the sizes of polyaniline complexes in water are independent of the molecular mass of the polyelectrolyte matrix and its chemical structure.     

Crystal structure analysis of polyethylene with electron diffraction intensity data: Deconvolution of multiple scattering effects

Recent determinations of n-paraffin and polyethylene crystal structures from electron diffraction data have claimed chain setting angles different from those reported for n-hexatriacontane. Re-evaluation of these data show that these determinations must be questioned because the intensities used were badly marred by multiple scattering. Due to the complexity of this phenomenon, efforts to deconvolute this error source are only partially successful. An independent structure determination for mostly unilamellar crystals of very low molecular weight polyethylene with data less affected by multiple scattering indicates that the atomic coordinates originally proposed for polyethylene in the earliest X-ray structure can still be justified.     

Surface Characteristics of Kaolinite and Other Selected Two Layer Silicate Minerals

The electrokinetic features and interfacial water structure, as revealed from molecular dynamics simulations (MDS) are considered with respect to the anisotropic features of selected two layer silicate minerals. Planar structures of kaolinite and antigorite are compared to the, compositionally equivalent, tubular structures of halloysite and chrysotile with respect to the pH dependency of zeta potential as determined from the electrophoretic mobility measurements. The importance of the atomic mismatch between the tetrahedral and octahedral sheets in a particular bilayer is discussed in order to explain the electrokinetic behaviour of these two layer silicate minerals. Interfacial water structure from MDS suggests that the silica tetrahedral surface is not wetted by water. In the case of planar silicates structural imperfections are considered to explain wetting characteristics. The possibility of polarity reversal (domain inversion) within a tetrahedral/octahedral layer and an out‐of‐order layer (inserted layer) within the tetrahedral/octahedral stack are considered in order to explain electrokinetic behaviour and wetting characteristics.     

Predicted Mechanism for Enhanced Durability of Zinc Containing Silicate Glasses

Experimental studies have reported that zinc oxide improves the durability of glasses used for nuclear waste immobilization. Here, molecular dynamics simulations are used to predict the atomic structures of sodium silicate glass with and without zinc. A simulated melt‐quench procedure is used to generate glass structures. Pair distribution functions, ring size distributions, and alkali clustering are then examined. This allows insights into the structural role of zinc oxide within the glass and helps distinguish between its reported functions as a network former and a network modifier. Changes in the sodium ion distribution and clustering behavior within the glass are observed, due to zinc oxide addition. This affects the local and intermediate‐range structure of the glass and provides a possible explanation for enhanced durability.     

Multiscale Modeling of Amyloid Fibrils Formed by Aggregating Peptides Derived from the Amyloidogenic Fragment of the A-Chain of Insulin

Computational prediction of molecular structures of amyloid fibrils remains an exceedingly challenging task. In this work, we propose a multi-scale modeling procedure for the structure prediction of amyloid fibrils formed by the association of ACC_1-13 aggregation-prone peptides derived from the N-terminal region of insulin’s A-chain. First, a large number of protofilament models composed of five copies of interacting ACC_1-13 peptides were predicted by application of CABS-dock coarse-grained (CG) docking simulations. Next, the models were reconstructed to all-atom (AA) representations and refined during molecular dynamics (MD) simulations in explicit solvent. The top-scored protofilament models, selected using symmetry criteria, were used for the assembly of long fibril structures. Finally, the amyloid fibril models resulting from the AA MD simulations were compared with atomic force microscopy (AFM) imaging experimental data. The obtained results indicate that the proposed multi-scale modeling procedure is capable of predicting protofilaments with high accuracy and may be applied for structure prediction and analysis of other amyloid fibrils.     

π-Conjugated cyanostilbene derivatives: a unique self-assembly motif for molecular nanostructures with enhanced emission and transport

π-Conjugated organic molecules represent an attractive platform for the design and fabrication of a wide range of nano- and microstructures for use in organic optoelectronics. The desirable optical and electrical properties of π-conjugated molecules for these applications depend on their primary molecular structure and their intermolecular interactions such as molecular packing or ordering in the condensed states. Because of the difficulty in satisfying these rigorous structural requirements for photoluminescence and charge transport, the development of novel high-performance π-conjugated systems for nano-optoelectronics has remained a challenge. This Account describes our recent discovery of a novel class of self-assembling π-conjugated organic molecules with a built-in molecular elastic twist. These molecules consist of a cyano-substituted stilbenic π-conjugated backbone and various terminal functional groups, and they offer excellent optical, electrical, and self-assembly properties for use in various nano-optoelectronic devices. The characteristic "twist elasticity" behavior of these molecules occurs in response to molecular interactions. These large torsional or conformational changes in the cyanostilbene backbone play an important role in achieving favorable intermolecular interactions that lead to both high photoluminescence and good charge carrier mobility in self-assembled nanostructures. Conventional π-conjugated molecules in the solid state typically show concentration (aggregation) fluorescence quenching. Initially, we describe the unique photoluminescence properties, aggregation-induced enhanced emission (AIEE), of these new cyanostilbene derivatives that elegantly circumvent these problems. These elastic twist π-conjugated backbones serve as versatile scaffolds for the preparation of well-defined patterned nanosized architectures through facile self-assembly processes. We discuss in particular detail the preparation of 1D nanowire structures through programmed self-assembly. This Account describes the importance of utilizing AIEE effects to explore optical device applications, such as organic semiconducting lasers (OSLs), optical memory, and sensors. We demonstrate the rich electronic properties, including the electrical conductivity, field-effect carrier mobility, and electroluminescence of highly crystalline 1D nanowire and coaxial donor-acceptor nanocable structures composed of elastic twist π-conjugated molecules. The electronic properties were measured using various techniques, including current-voltage (I-V), conducting-probe atomic force microscopy (CP-AFM), and space-charge-limited-current (SCLC) measurements. We prepared and characterized several electronic device structures, including organic field-effect transistors (OFETs) and organic light-emitting field-effect transistors (OLETs).     

Phase separation of polystyrene-b-(ethylene-co-butylene)-b-styrene (SEBS) deposited on polystyrene thin films

Phase separation of a triblock copolymer, polystyrene-b-(ethylene-co-butylene)-b-styrene (SEBS) on the thin films of a homopolymer, polystyrene (PS), was studied by atomic force microscopy (AFM) and transmission electron microscopy (TEM). The final morphology after phase separation was found to be greatly dependent on the relation between the molecular weight of the PS block and homo-PS. Dispersed spherical and worm-like micelles of SEBS were observed when the molecular weight of homo-PS is smaller than the PS block in SEBS, while large structures with inner micro-phase separation of SEBS was found when the molecular weight of homo-PS was much higher than that of the PS block. The origin of such a change in morphology is attributed to the difference of structure and interfacial tension at the interface between the matrix homo-PS and the PS block in SEBS triblock copolymer assembly.     

Crystal structure of the high-alkaline serine protease PB92 from Bacillus alcalophilus

The crystal structure of a serine protease from the alkalophilicstrain Bacillus alcalophilus PB92 has been determined by X-raydiffraction at 1.75 Â resolution. The structure has beensolved by molecular replacement using the atomic model of subtilisinCarlsberg. The model of the PB92 protease has been refined toan R-factor of 14.0% and contains 1882 protein atoms, two calciumions and 188 water molecules. The overall folding of the polypeptide chain closely resembles that of the subtilisins. Furthermore,almost all of the secondary structure elements found in subtilisinCarlsberg are also present in the PB92 protease. The major differencesbetween the two structures are located around the deletion regions(residues 37 and 158–161 in subtilisin Carlsberg) andin two loops which are known to be the most variable parts ofsubtilisin structures. Flexibility of one of these loops (residues126–130 in the PB92 protease) is believed to account forthe inducedfit mechanism of substrate binding.