Equivalent potential of water molecules for electronic structure of glutamic acid

The fundamental importance of the electronic structure of molecules is widely recognized. To get reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. Here, the first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of glutamic acid, which is a hydrophilic amino acid and is negatively charged (Glu(-)) in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Glu(-) and water molecules is calculated by free cluster calculation. Then, based on the geometric structure, the electronic structure of Glu(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Glu(-) with the potential of dipoles is calculated. Our calculations show that the major effect of water molecules on Glu(-)'s electronic structure is lowering the occupied electronic states by about 0.017 Ry, and broadening energy gap by 12%. The effect of water molecules on the electronic structure of Glu(-) can be well simulated by dipoles potential.     

高分子结构与性能关系原理-结构层次的意义

高分子结构是高分子性能的重要物质基础,对其结构进行合理的划分,有助于准确把握高分子物理知识体系的内在脉络。高分子结构层次的划分不仅要思考静态时特定质点在空间的堆砌特征,而且也要考虑结构出现运动或是变化的基本单元。按照质点尺度的不同,高聚物的结构可以分为单一高分子结构(链结构)、多个高分子结构(凝聚结构)和多种高分子结构(织态结构)三个主要层次。其中,化学因素所确定的链结构层次包括相对分子质量以及构造、构型等同分异构体形式;物理因素所确定的结构层次为高分子局部质点集合在空间的堆砌和排列;链段是容易被忽视、但又是最为重要的运动(变化)单元。     

Polyvinyl alcohol hydrogels I. Microscopic structure by freeze-etching and critical point drying techniques

Froeze-etching (FE) and critical point drying (CPD) techniques were employed to prepare samples for investigating surface and bulk structures of polyvinyl alcohol (PVA) hydrogels by scanning electron microscopy. The hydrogels were obtained by freezing homogeneous solutions containing PVA polymer in either water or an aqueous solution of dimethyl sulfoxide (DMSO). An oriented porous structure was observed in the PVA hydrogel prepared without DMSO. The structure on the surface was found to be more porous than in the bulk for PVA hydrogels prepared from aqueous DMSO solutions. For given compositions of the hydrogels, samples prepared by FE technique showed a highly porous fibrillar structure on the surface, while those prepared by CPD technique showed a collapsed fibrillar structure with much less porosity. This marked difference indicates a collapse of the surface structure caused by the CPD technique. The CPD technique also led to significant reduction in porosity and loss of fibrillar structure in the bulk. Volume shrinkage of hydrogels caused by dehydration in ethanol may be responsible for the surface collapse as well as alteration of bulk structure. The FE technique reveals a more native structure of hydrogels than the commonly used CPD technique. However, it suffers from disadvantages such as charging and structural damage at high magnifications.     

Preparation of cuprite (Cu2O), paramelaconite (Cu32+Cu21+O4) and tenorite (CuO) with magnetron sputtering ion plating: characterization by EPMA, XRD, HEED and SEM

Cu-O layers were deposited on Si-<100> wafers at 90°?C by means of reactive magnetron sputtering ion plating (R-MSIP). A Cu-target was sputtered in rf-mode by an oxygen/argon plasma, and the influence of the oxygen partial pressure on composition, structure, texture and morphology of the Cu-O layers was investigated. The analysis with EPMA, XRD, HEED and SEM yielded the following results: with an appropriate setting of the oxygen partial pressure, the oxygen content of the films could be controlled between 0 and 50 at-%. XRD bulk structure analysis shows changes in the crystal structure of the films with increasing oxygen content from the fcc structure of Cu, followed by the sc structure of Cu₂O (cuprite), the tetragonal structure of Cu₃ ²⁺Cu₂ ¹⁺O₄ (paramelaconite) to the monoclinic structure of CuO (tenorite). As revealed by HEED, the structure of the near-surface region of the latter two is the same as that of the bulk, whereas in the case of the films with fcc bulk structure, due to oxidation by air, the surface has the sc structure of Cu₂O, and in the case of the film with the sc structure, a monoclinic surface structure of CuO is observed. SEM analyses detected a disordered columnar growth of all Cu-O films.     

The equivalent potential of water for electronic structure of aspartic acid

The equivalent potential of water for the electronic structure of aspartic acid (Asp(-)) in solution is constructed by the first-principles, all-electrons, ab initio calculations. Aspartic acid is a hydrophilic amino acid which is negatively charged in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Asp(-) and water molecules is calculated by the free cluster calculation. Then, based on the obtained geometric structure, the electronic structure of Asp(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Asp(-) with the potential of dipoles is calculated. The results show that the major effect of water on Asp(-)'s electronic structure is lowering the occupied molecular orbitals by about 0.02 Ry on average, and narrowing energy gap by 10.8%. The effect of water on the electronic structure of Asp(-) can be simulated by dipoles potential.     

Kinetic pathway to double-gyroid structure

We have investigated the structural development during order-order transitions to the double-gyroid (DG) phase of nonionic surfactant/water systems based on two-dimensional small-angle x-ray scattering patterns from highly oriented ordered mesophases. The lamellar (L) to DG transition proceeds through two intermediate structures, a fluctuating perforated layer structure having ABAB stacking and a hexagonal perforated lamellar structure with ABCABC stacking (HPLABC). For a hexagonally packed cylinder (H) to DG transition, we also observed the HPLABC structure as the intermediate phase, thus the HPLABC is an entrance structure for the DG phase. The hexagonal perforated lamellar (HPL) structure consists of hexagonally packed holes surrounded by the planar tripods, and the transition from HPL structure to the DG phase proceeds by rotation of the dihedral angle of connected tripods. A geometrical consideration shows that large deformations of HPL planes are necessary to form the DG structure from the HPLABC structure, whereas the transition from a HPL structure with ABAB stacking (HPLAB) to the DG structure is straightforward. In spite of the topological constraints, the HPLABC structure is observed in the kinetic pathway to the DG structure.     

辽河减压渣油中非卟啉镍的XAFS研究

为获得石油中非卟啉Ni的结构信息，采用荧光法对辽河减压清油中非叶琳Ni的 K边进行了XAFS测试非叶琳Ni第一配位壳层的结构和Ni-四苯基卟啉（NiTPP）的配 位结构类似，也是4个氮原子，呈平面四方构型为0.192nm，在较高的配位壳层，二 者存在一定的差别此外，根据XAFS测试，对石油中非卟啉Ni讨论.     

Synthesis of polyacrylate core-shell structure latex by radiation techniques

A series of poly(butyl acrylate-co-methyl methacrylate)/poly (ethyl acrylate-co-acrylic acid) interpenetrating polymer network (IPN) was synthesized in latex form by emulsion polymerization. The multiphase morphology of the latex particles was studied after two-stage polymerization by using transimission electron microscope (TEM), the result indicated that the morphology of the particles comprises gradient shell structure, cellular structure and core-shell structure. The change of morphology might stem from emulsion polymerization by radiation initiation or chemical initiation and the weight composition of poly(EA-co-MMA) seed latex which formed the core. By radiation techniques, we successfully synthesized poly( BA-co-MMA)/poly(EA-co-AA) latex of core-shell structure having (42-8)/(46-4) weight compositions. The PA core-shell structure latex applied to textile as a water proofing coating showed higher water-pressure and easier handling than that with PA homogeneous phase structure latex.     

High-field 1H MAS and 15N CP-MAS NMR studies of alanine tripeptides and oligomers: distinction of antiparallel and parallel beta-sheet structures and two crystallographically independent molecules

beta-Strand peptides are known to assemble into either antiparallel (AP) or parallel (P) beta-sheet forms which are very important motifs for protein folding and fibril formations occurring in silk fibroin or amyloid proteins. Well-resolved 1H NMR signals including NH protons were observed for alanine tripeptides (Ala)3 with the AP and P structures as well as (Ala)n (n = 4-6) by high-field/fast magic-angle spinning NMR. Amide NH and amino NH3+ 1H signals of (Ala)3 with the P structure were well resonated at 7.5 and 8.9 ppm, respectively, whereas they were not resolved for the AP structure. Notably, NH 1H signals of (Ala)3 and (Ala)4 taking the P structure are resonated at higher field than those of the AP structure by 1.0 and 1.1 ppm, respectively. Further, NH 15N signals of (Ala)3 with the AP structure were resonated at lower field by 2 to 5 ppm than those of (Ala)3 with the P structure. These relative 1H and 15N hydrogen bond shifts of the P structure with respect to those of the AP structure are consistent with the relative hydrogen bond lengths of the interstrand N-H...O=C bonds. Distinction between the two crystallographically independent chains present in the AP and P structures was feasible by 15N chemical shifts but not by 1H chemical shifts because of insufficient spectral resolution in the latter. Calculated 1H and 15N shielding constants by density functional theory are generally consistent with the experimental data, although some discrepancies remain depending upon the models used.     

Supramolecularly engineered perylene bisimide assemblies exhibiting thermal transition from columnar to multilamellar structures

Perylene 3,4:9,10-tetracarboxylic acid bisimide (PBI) was functionalized with ditopic cyanuric acid to organize it into complex columnar architectures through the formation of hydrogen-bonded supermacrocycles (rosette) by complexing with ditopic melamines possessing solubilizing alkoxyphenyl substituents. The aggregation study in solution using UV-vis and NMR spectroscopies showed the formation of extended aggregates through hydrogen-bonding and π-π stacking interactions. The cylindrical fibrillar nanostructures were visualized by microscopic techniques (AFM, TEM), and the formation of lyotropic mesophase was confirmed by polarized optical microscopy and SEM. X-ray diffraction study revealed that a well-defined hexagonal columnar (Col(h)) structure was formed by solution-casting of fibrillar assemblies. All of these results are consistent with the formation of hydrogen-bonded PBI rosettes that spontaneously organize into the Col(h) structure. Upon heating the Col(h) structure in the bulk state, a structural transition to a highly ordered lamellar (Lam) structure was observed by variable-temperature X-ray diffraction, differential scanning calorimetry, and AFM studies. IR study showed that the rearrangement of the hydrogen-bonding motifs occurs during the structural transition. These results suggest that such a striking structural transition is aided by the reorganization in the lowest level of self-organization, i.e., the rearrangement of hydrogen-bonded motifs from rosette to linear tape. A remarkable increase in the transient photoconductivity was observed by the flash-photolysis time-resolved microwave conductivity (FP-TRMC) measurements upon converting the Col(h) structure to the Lam structure. Transient absorption spectroscopy revealed that electron transfer from electron-donating alkoxyphenyl groups of melamine components to electron-deficient PBI moieties takes place, resulting in a higher probability of charge carrier generation in the Lam structure compared to the Col(h) structure.     

Quantum chemistry can locally improve protein crystal structures

We have re-refined the X-ray structure of the heme site in cytochrome c553, supplementing the crystallographic data with quantum chemical geometry optimizations, instead of the molecular mechanics force field used in standard crystallographic refinement. By comparing the resulting structure, obtained using medium-resolution data (170 pm), with an atomic-resolution structure (95 pm) of the same protein, we show that the inclusion of quantum chemical information into the refinement procedure improves the structure significantly. Thus, errors in the Fe-ligand distances are reduced from 3 to 32 pm in the low-resolution structure to 0-5 pm in the re-refined structure, one side-chain atom changes its conformation (a movement by 214 pm toward its position in the high-resolution structure), and the R factors are improved by up to 0.018. Thus, quantum refinement may be a powerful method to obtain an accurate structure for interesting parts of a protein.     

Preparation of spherical nanostructured poly(methacrylic acid)/PbS composites by a microgel template method

Spherical poly(methacrylic acid)/PbS (PMAA/PbS) composites with a fishnet-like surface and core-shell structure were prepared by a microgel template method. The composites were prepared in two steps. Pb(Ac)(2) was dissolved in MAA solution before it was polymerized into microgels in an inverse suspension system. In this way, Pb(2+) was trapped within the microgel network. Then, H(2)S was introduced slowly into the system, and the metal ions were deposited within the microgels as PbS. The presence of PbS was confirmed by X-ray diffraction (XRD) and thermogravimetric measurements, and the morphology of the composites was characterized by scanning electron microscopy (SEM). It was found that the surface structure of the microparticles depends largely on the nature of the continuous phase of the system. The microparticles from xylene have a fishnet-like surface structure, and the inner structure and composition of the particles are different from the outer structure and composition. The surface of the particles from cyclohexane, however, appears smoother and denser than the surface of the particles from xylene. The different structure of the particle surfaces from the two systems has been attributed to the differences in template structure.     

Preparation of Pt/Rh bimetallic colloidal particles in polymer solutions using borohydride-reduction

Colloidal dispersions of Pt/Rh bimetallic particles have been synthesized by the reduction of Pt(IV)/Rh(III) ionic solutions by using borohydride-reduction in the presence of poly(N-vinyl-2-pyrrolidone). The size and the structure of the synthesized particles have been examined by transmission electron micrograph (TEM) and extended X-ray absorption fine structure (EXAFS). We have succeeded in producing the bimetallic Pt/Rh particles with an average diameter of 2.8 nm in polymer solutions by the stepwise addition of sodium borohydride aqueous solution. The distribution of different metallic species in a particle tended to be "cluster-in-cluster" structure, in contrast to the bimetallic particle with an average diameter of 1.4 nm synthesized by alcohol-reduction which have a core-shell structure.     

SrSn4: a superconducting stannide with localized and delocalized bond character

The title compound is the tin-richest phase in the system Sr-Sn and is obtained by stoichiometric combination of the elements. SrSn(4) peritecticly decomposes under formation of SrSn(3) and Sn at 340 degrees C. The structure determined from a single crystal shows a new structure type with a novel structure motive in tin chemistry. It can be described by a corrugated, distorted quadratic net of tin atoms as the only building unit. The nets intersect at common Sn atoms, and the resulting channels host the Sr atoms. The structure can alternatively be described as an intergrowth structure of the AlB(2)-type and W-type. The atoms that are connected by the two shortest Sn-Sn distances (2.900 and 3.044 A) form a two-dimensional net consisting of hexagons of tin atoms. The hexagons have boat conformation in contrast to the rather similar alpha-As structure type, where hexagons have a chair conformation. Further tin atoms connect the two-dimensional net of Sn hexagons. Temperature-dependent magnetic susceptibility measurements show that SrSn(4) is superconducting with T(c) = 4.8 K at 10 G. LMTO band structure and density of states calculations verify the metallic behavior of SrSn(4). An analysis of the electronic structure with the help of the electron localization function (ELF) shows that localized covalent bonds beside delocalized bonds coexist in SrSn(4).     

Hexanuclear cobalt carbonyl carbide clusters: the interplay between octahedral and trigonal prismatic structures

The six-vertex cobalt carbonyl clusters [Co6C(CO)n](2-) (n = 12, 13, 14, 15, 16) with an interstitial carbon atom have been studied by density functional theory (DFT). These DFT studies indicate that the experimentally known structure of [Co6C(CO)15](2-) consisting of a Co6 trigonal prism with each of its edges bridged by carbonyl groups is a particularly stable structure lying more than 20 kcal/mol below any other [Co6C(CO)15](2-) structure. Addition of a CO group to this [Co6C(CO)15](2-) structure gives the lowest energy [Co6C(CO)16](2-) structure, also a Co6 trigonal prism with one of the vertical edges bridged by two CO groups and the remaining eight edges each bridged by a single CO group. However, this [Co6C(CO)16](2-) structure is thermodynamically unstable with respect to CO loss reverting to the stable trigonal prismatic [Co6C(CO)15](2-). This suggests that 15 carbonyl groups is the maximum that can be attached to a Co6C skeleton in a stable compound. The lowest energy structure of [Co6C(CO)14](2-) has a highly distorted octahedral Co6 skeleton and is thermodynamically unstable with respect to disproportionation to [Co6C(CO)15](2-) and [Co6C(CO)13](2-). The lowest energy [Co6C(CO)13](2-) structure is very similar to a known stable structure with an octahedral Co6 skeleton. The lowest energy [Co6C(CO)12](2-) structure is a relatively symmetrical D3d structure containing a carbon-centered Co6 puckered hexagon in the chair form.     

Water structure and its influence on the flotation of carbonate and bicarbonate salts

Interfacial water structure is a most important parameter that influences the collector adsorption by salt minerals such as borax, potash and trona. According to previous studies, salts can be classified as water structure makers and water structure breakers. Water structure making and breaking properties of salt minerals in their saturated brine solutions are essential to explain their flotation behavior. In this work, water structure making-breaking studies in solutions of carbonate and bicarbonate salts (Na(2)CO(3), K(2)CO(3), NaHCO(3) and NH(4)HCO(3)) in 4 wt% D(2)O in H(2)O mixtures have been performed by FTIR analysis of the OD stretching band. This method reveals a microscopic picture of the water structure making/breaking character of the salts in terms of the hydrogen bonding between the water molecules in solution. The results from the vibrational spectroscopic studies demonstrate that carbonate salts (Na(2)CO(3) and K(2)CO(3)) act as strong structure makers, whereas bicarbonate salts (NaHCO(3) and NH(4)HCO(3)) act as weak structure makers. In addition, the changes in the OD band parameters of carbonate and bicarbonate salt solutions are in agreement with the viscosity characteristics of their solutions.     

Characterization of the surface structure of gold nanoparticles and nanorods using structure sensitive reactions

The surface structure of gold nanorods has been determined by studying the behavior of electrochemical reactions sensitive to the structure and compared to that obtained by other structure characterization techniques. Lead underpotential deposition (UPD) reveals that the surface of the nanorods is composed by (111) and (110) domains, while (100) domains are practically absent from the surface. In the case of the oxygen reduction reaction, the formation of hydrogen peroxide as a final product of the reaction in the whole potential range also indicates that (100) domains are absent on the surface of the nanoparticles, corroborating the previous result. These results are compared with other surface structure information provided by other techniques.     

Fibril formation of 1,3:2,4-di(3,4-dimethylbenzylidene) sorbitol in a polypropylene melt

Binary mixtures of 1,3:2,4-di(3,4-dimethylbenzylidene) sorbitol (DMDBS) within the melt of polypropylene (PP) were studied at DMDBS contents of 0.4 and 1.0 wt %. DMDBS serves as a nucleating agent in PP crystallization by formation of a nanofibrillar network. The kinetics of the DMDBS solidification process within the PP melt and the ensuing nanofibrillar structure were studied by in situ small-angle X-ray scattering (SAXS) analysis combined with imaging by electron microscopy. The dynamic lag of the fibrillar structure formation kinetics and its temperature dependence indicate a nucleation and growth mechanism, controlled by the rate of nucleation. Investigation of the fibrillar structure by electron microscopy indicates a complex structure in which long and thin fibrils (less than 100 nm in cross-section) are composed of thinner nanofibrils (less than 10 nm in cross-section).     

Rings-on-a-string chain structure in DNA

Using fluorescence microscopy (FM), which permits the observation of single molecules, we found that a pearling structure is generated on a single long DNA molecule upon the addition of a gemini (dimeric) surfactant. This pearling structure was further investigated by performing atomic force microscopy measurements on the same DNA molecules as observed by FM. These observations revealed that the pearling structure is composed of many rings that are interconnected by elongated coil parts along a single DNA molecule, i.e., rings-on-a-string structure. The mechanism of the formation of such an intrachain segregated structure in terms of microphase separation on a single polyelectrolyte chain is discussed.