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.     

Applications of a HOUDINI-based structure elucidation system

SESAMI, a comprehensive program for the elucidation of the structure of complex compounds of carbon, incorporates a structure reduction-based structure genearator (COCOA). Observed limitations with this program in the solution of higher molecular weight unknowns prompted the development of a structure generator (HOUDINI) which embodies a new concept, convergent structure generation. A comparison of the performance of COCOA-based and HOUDINI-based SESAMI using a set of complex, naturally occurring compounds as a test set of unknowns revealed faster execution times and more efficient processing of ambiguous structural information for the latter.     

The C5SiMe7+ cation: pyramidal,bicyclic, or cyclohexadienyl?

The monosila analogue of the C6Me7+ cation can be accessed by hydride abstraction from (pentamethylcyclopentadienyl)dimethylsilane, Cp*SiMe2H. Treatment of this material with triphenylmethylium tetrakis(pentafluorophenyl)borate in dichloromethane at -50 degrees C produced a single cationic species stable for a day or longer. The presence of a single resonance for the ring methyls and a single resonance for the silyl methyls in both the 1H and the 13C spectra indicated either a static structure with fivefold symmetry or a dynamic structure in which the dimethylsilyl group equilibrates rapidly among positions. Density function theory calculations found a minimum whose structure had the unsymmetrical silabicyclo[3.1.0]hexenyl structure. Calculated 1H, 13C, and 29Si chemical shifts for this structure were in good agreement with the observed values for this structure. Another calculated minimum was the silacyclohexadienyl structure, but its calculated chemical shifts were very different from those observed. We conclude that the cation has the bicyclic structure but rapidly interconverts the ring positions to produce the very simple NMR spectra.     

Predicting RNA secondary structure by free energy minimization

RNA structure is hierarchical. Secondary structure contacts, i.e. the canonical base pair contacts, are generally stronger and form faster than the tertiary structure. Therefore, RNA secondary structures can be predicted independently of tertiary structure prediction. Furthermore, the stability of a given RNA secondary structure can be quantified using nearest neighbor free energy parameters. These parameters are the basis of a number of free energy minimization algorithms that predict RNA secondary structure for either a single sequence or multiple sequences. This article reviews the progress of RNA secondary structure prediction by free energy minimization and describes many of the algorithms that have been developed.     

Structural transition of nematic liquid crystal in cylindrical capillary as a result of the annihilation of two point defects

We study the annihilation of hedgehog-antihedgehog defects in confined nematic liquid crystals using Brownian molecular dynamics simulations. After the collision, merging of defects, and building a loop disclination structure, system can experience a structural transition into another nematic structure, triggered by a nucleation of loop disclination structure. In our rough theoretical approach we calculate the size of the emerged loop structure as the function of the typical size of the confining cavity. Attention is paid also to the dynamics of the loop structure after collision.     

Architecture of intracellular networks in plant matrices

Pectin is an integral component of plant cell walls. It is believed to form an interconnected network structure independent of the cellulose–xyloglucan network structure. Pectin gels are often used as a model for the pectin network structure within the plant cell wall. The middle lamella pectin can be extracted with chelating agents and is believed to be associated through cooperative binding of calcium ions in the so-called egg-box junction zones. Although a great deal is known about the nature of the junction zones in pectin gels, less is known about the long-range structure within calcium-set gels. Two plausible alternative models for long-range order in these gels are a pseudo rubber-like structure and a fibrous network structure. Atomic force microscopy studies of calcium-induced gel precursors, and fragments released from gels, suggest that association leads to a branched fibrous structure within the gels. Enzymatic de-esterification of high methoxy pectin in the presence of calcium ions can induce gelation of the pectin. Thus pectin gel networks may provide a model for a self-assembled network structure within the middle lamella region of the plant cell wall.     

Inorganic Crystal Structure Data to be Presented in a Form More Useful for Further Studies

To make inorganic structure data more useful for further studies a five-point list of simple procedures to be followed by authors of crystal structure papers is proposed. 1. A crystal structure should be described with the space group corresponding to its true symmetry. 2. A new structure proposal should be tested, if it is realistic in principle. 3. A structure should be described with a space group in a setting given in the International Tables. 4. For a comparison with other structures the structure data should be standardized with the program STRUCTURE TIDY. 5.“New” structure data should be checked in the databases, Chemical Abstracts or on-line intemet resources, if they are really new. The list is supplemented with many explanations, commentaries, examoles and references.     

纳米粒子驱动受限环境下两嵌段共聚物/均聚物混合体系的自组装行为

采用含时金兹堡-朗道理论(time-dependent ginzburg-landau theory,简称TDGL)方法研究了纳米粒子(nanoparticles,简称NPs)掺杂的两嵌段共聚物/均聚物(AB/C)共混体系在球形受限下的自组装行为.在不同球形受限条件下,两嵌段共聚物/均聚物共混体系形成了多种丰富的形貌,如双螺旋结构、单螺旋结构、层状结构和洋葱环状结构等.当在以上前3种体系中掺杂纳米粒子后,体系结构发生了很大的变化.详细研究了纳米粒子的浓度和浸润强度对以上结构的影响.研究结果表明,通过调控纳米粒子的浓度和浸润性质,该共混体系实现了双螺旋结构→层状结构,单螺旋结构→双螺旋结构,层状结构→单螺旋结构等多种取向序的转变.对于洋葱环状结构,纳米粒子的加入对体系这一结构的影响不大.     

三维纳米液膜沉积结构的模拟研究

基于三维动力学蒙特卡罗模型,再现了纳米液膜干燥后形成的双尺度沉积结构,探究了液体化学势、纳米粒子移动速率、液体临界蒸发率以及化学势锐度等参数对纳米液膜沉积结构的影响。结果表明,纳米液膜干燥时,液膜中的纳米粒子随着三相线移动自组装形成各种各样的沉积结构沉积在基板上。纳米液膜蒸发过程中,当液体蒸发达到临界蒸发率时液体化学势将发生突变,使其形成两种沉积结构。随液体初始化学势的增大,沉积结构逐渐变为均匀分布的密集网状结构。液体临界蒸发率越小,液体化学势突变后形成的沉积结构越明显。纳米粒子的移动速率越快,沉积结构中的枝状结构越少。化学势锐度对双尺度沉积结构的差异有很大的影响,锐度越大,两种沉积结构的差异越大。     

Experimental and theoretical investigation on the relative stability of the PdS2- and pyrite-type structures of PdSe2

Under ambient condition PdSe2 has the PdS2-type structure. The crystal structure of PdSe2 under pressure (up to 30 GPa) was investigated at room temperature by X-ray diffraction in an energy-dispersive configuration using a diamond anvil cell with a mixture of water/ethanol/methanol as a pressure transmitting medium. A reversible structural transition from the PdS2-type to the pyrite-type structure occurs around 10 GPa, and the applied pressure reduces the spacing between adjacent 2/proportional to [PdSe2] layers of the PdS2-type structure to form the three-dimensional lattice of the pyrite-type structure. First principles and extended Hückel electronic band structure calculations were carried out to confirm the observed pressure-induced structural changes. We also examined why the isoelectronic analogues NiSe2 and PtSe2 adopt structures different from the PdS2-type structure on the basis of qualitative electronic structure considerations.     

Etude par diffraction des rayons X des structures rencontrees dans les solutions aqueuses concentrees d'un polyelectrolyte amphipathique

Low and wide-angle X-ray diffraction was used to study the structure of aqueous gels of a maleic anhydride-hexadecylvinylether alternating copolymer, as a function of water content, degree of neutralization and temperature. Two types of structure have been found: a lamellar structure observed at low degrees of neutralization and a cylindrical structure observed at high degrees of neutralization. In both cases, the structural parameters have been analysed.     

Structural and Electronic Peierls Distortions in the Elements (A): The Crystal Structure of Tellurium

The thermodynamically stable tellurium phase (standard conditions) in the trigonal α‐Se structure type may be understood to arise from a three‐dimensional Peierls distortion away from a simple cubic structure. Three‐dimensional electronic structure calculations from first principles reveal that the simple cubic structure exhibits partially filled bands which are folded back when using a hexagonal coordinate system with a tripled volume. The symmetry‐lowering transition from the cubic to the experimentally observed structure is paralled by a removal of band degeneracies and crossings, opening a band gap at the Fermi level.     

Influence of Gamma-Irradiation and Thermal Annealing on Molecular–Topological Structure of Tetrafluoroethylene–Ethylene Copolymer

The molecular–topological structure of a tetrafluoroethylene copolymer with ethylene after γ-irradiation and thermal annealing has been studied. The pseudo-network structure of the copolymer contains, in addition to the amorphous block, crystalline segments of macromolecules in the role of branching sites. Topologically, the diblock structure of the copolymer after thermal annealing at 538 K is transformed into a three-block structure with the appearance of a high-temperature amorphous block. Irradiation of the copolymer with γ-rays to a dose of 150 kGy does not lead to appreciable changes in its molecular–topological 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.     

Effect of salts on water viscosity in narrow membrane pores

The effect of various salts on the viscosity, and by implication structure, of water in polymeric membrane pores of radius approximately 1.69 nm and low charge density has been studied. Permeation of pure water and various electrolyte solutions was analyzed using the Hagen-Poiseuille equation expressed in a ratio form to exclude membrane-specific quantities such as pore radius and length. The analysis produced viscosity ratios of electrolyte to pure water inside the membrane pores. Comparing the viscosity ratios inside the pores with their bulk counterparts showed that confinement significantly increased the sensitivity of water structure to the presence of ions. It has been found that, in relative terms in the pores, Cl- was a strong structure breaker, K+ was a moderately strong structure breaker, Na+ was a weak structure breaker, SO4(2-) was a weak structure maker, and Mg2+ was a strong structure maker. Predictive modeling of membrane separation performance would benefit from such effects being taken into account in cases where the pore ion concentrations may be high.     

Structure generation by reduction: a new strategy for computer-assisted structure elucidation

A problem common to computer programs for structure elucidation is the efficient and prospective use of the input information to constrain the structure generation process. The input may consist of potentially overlapping substructure requirements and alternative substructure interpretations of spectral data. Other useful information may be structural features that must not be present in the output structures. All of these may interact in a complex manner that is impossible to determine by use of a bond-by-bond structure assembly algorithm. A new method is described called structure reduction. In contrast to structure assembly, this method begins with a set of all bonds and removes inconsistent bonds as structure generation progresses. This results in a more efficient use of the input information and the ability to use potentially overlapping required substructures. Several examples illustrate the application of our computer program COCOA, which uses this method to solve real-world structure elucidation problems.     

An alternative description of the paulingite structure

The paulingite structure can be described as an invariant transformation of the gismondine structure. Packets of a fourling construction of the gismondine structures, which is closely related to the merlinoite structure, are used to build the structure of paulingite as an interpenetrating sixling.     

Effect of γ-irradiation and thermal annealing on the molecular–topological structure of a copolymer of tetrafluoroethylene and perfluoro(propyl vinyl ether)

The molecular–topological structure of a copolymer of tetrafluoroethylene and perfluoro(propyl vinyl ether) subjected to γ-irradiation and thermal annealing has been studied for the first time with the use of thermomechanical spectrometry. The pseudonetwork structure of the copolymer contains an amorphous block (interjunction chains) and crystalline segments (branching points). The diblock amorphous and crystalline structure with a crystal structure fraction of 0.21 transformed into an almost completely amorphous structure with a crystallite fraction of 0.06 after the irradiation of the copolymer at a dose of 600 kGy. Thermal annealing at 483 K formed a new structure: a high-temperature amorphous block.     

Structural identification of a novel degradant of the antibiotic pirlimycin formed under thermal stress conditions

The structure of a novel, thermally-induced degradant of the antibiotic pirlimycin is presented. The degradant was discovered during thermal stress stability testing of pirlimycin. The structure was determined using high resolution mass spectrometry, ms/ms fragmentation, and extensive nmr studies including a combination of homonuclear TOCSY and gradient, inverse-detected 2-D nmr experiments which included GHSQC and GHMBC. All nmr, high resolution ms and ms/ms fragmentation data are consistent with loss of a molecule of HCl during a ring closure involving one of the hydroxyl moieties from the sugar portion of the molecule forming a tetrahydrofurano[3,2-b]perhydropyran ring structure. The X-ray crystal structure is reported for pirlimycin. Using this structure molecular modelling studies are performed which demonstrate the feasibility of the formation of the new structure.