Open access article in Journal of Applied Crystallography

Crystallography Open Database – an open-access collection of crystal structures

Gražulis, S. — 2009-08-01

The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality.

Re-evaluation of formulae for X-ray stress analysis in polycrystalline specimens with fibre texture. Erratum

Yokoyama, R. — 2009-06-01

Errors in the paper by Yokoyama & Harada [J. Appl. Cryst. (2009), 42, 185–191] are corrected.

The pseudo-single-crystal method: a third approach to crystal structure determination

Kimura, T. — 2009-06-01

A novel method that enables single-crystal diffraction data to be obtained from a powder sample is presented. A suspension of LiCoPO4 microrods was subjected to a frequency-modulated dynamic elliptical magnetic field to align the microrods; the alignment achieved was consolidated by photopolymerization of the suspending UV-curable monomer. The composite thus obtained (referred to as a pseudo single crystal) gave rise to X-ray diffraction data from which the crystal structure was solved using the standard method for single-crystal X-ray analyses. The structure determined was in good agreement with that reported using a conventional single crystal.

Elastic constants of fibre-textured thin films determined by X-ray diffraction

Martinschitz, K.J. — 2009-06-01

A new methodology is presented that allows the rapid determination of elastic constants of cubic fibre-textured thin films by X-ray diffraction. The theoretical concept is developed and tested on calculated examples of Cu and CrN films. The mechanical elastic constants are extrapolated from X-ray elastic constants by taking into consideration crystal and macroscopic elastic anisotropy. The derived algorithm enables the determination of a reflection and the corresponding value of the X-ray anisotropic factor Γ for which the X-ray elastic constants are equal to their mechanical counterparts in the case of fibre-textured cubic polycrystalline aggregates. The approach is independent of the crystal elastic anisotropy and depends on the fibre-texture type, the texture sharpness, the number of randomly oriented crystallites and the supposed grain-interaction model. In the experimental part, out-of-plane Young's moduli of 111 and 311 fibre-textured Cu and CrN thin films deposited on monocrystalline Si(100) substrates are determined. The moduli are extrapolated from thin-film experimental X-ray elastic constants that are determined by a combination of X-ray diffraction substrate curvature and sin2ψ methods. For the calculation, the film macroscopic elastic anisotropy (texture) is considered. The advantage of the new technique lies in the fact that experimental moduli are determined nondestructively, using a static diffraction experiment, and represent volume-averaged quantities.

PDB_REDO: automated re-refinement of X-ray structure models in the PDB

Joosten, R.P. — 2009-06-01

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

Lecture demonstrations in a public lecture on `X-ray crystal structure analysis: from W. L. Bragg to the present day'

Helliwell, J.R. — 2009-04-01

Constraints and restraints in crystal structure analysis

Immirzi, A. — 2009-04-01

The widely used restraint-based approach to structural analysis using diffraction data is critiqued. The convenience of using rigid constraints, through the use of internal coordinates, is discussed.

Synthesis and physical properties of ferrocene derivatives. XXI. Crystal structure of a liquid crystalline ferrocene derivative, 1,1'-bis[3-[4-(4-methoxyphenoxycarbonyl)phenoxy]propyloxycarbonyl]ferrocene

Okabe, T. — 2009-02-01

The crystal structure of the title 1,1′-disubstituted ferrocene derivative was determined by X-ray diffraction using a single crystal. This compound exhibits a nematic phase only. The X-ray structure analysis revealed that the two substituents lie in the same direction (`U' shape) and the flexible spacer adopts a gauche conformation. These conformations are strongly related to the formation of a rod-like shape, which favors liquid crystalline behavior. In the crystal structure, C—H⋯π, π–π and T-stacking interactions were observed. It is considered that these interactions play a major role in stabilizing the molecular packing arrangement and the mesomorphism.

Odd electron diffraction patterns in silicon nanowires and silicon thin films explained by microtwins and nanotwins

Cayron, C. — 2009-04-01

Odd electron diffraction patterns (EDPs) have been obtained by transmission electron microscopy (TEM) on silicon nanowires grown via the vapour–liquid–solid method and on silicon thin films deposited by electron beam evaporation. Many explanations have been given in the past, without consensus among the scientific community: size artifacts, twinning artifacts or, more widely accepted, the existence of new hexagonal Si phases. In order to resolve this issue, the microstructures of Si nanowires and Si thin films have been characterized by TEM, high-resolution transmission electron microscopy (HRTEM) and high-resolution scanning transmission electron microscopy. Despite the differences in the geometries and elaboration processes, the EDPs of the materials show great similarities. The different hypotheses reported in the literature have been investigated. It was found that the positions of the diffraction spots in the EDPs could be reproduced by simulating a hexagonal structure with c/a = 12(2/3)1/2, but the intensities in many EDPs remained unexplained. Finally, it was established that all the experimental data, i.e. EDPs and HRTEM images, agree with a classical cubic silicon structure containing two microstructural defects: (i) overlapping Σ3 microtwins which induce extra spots by double diffraction, and (ii) nanotwins which induce extra spots as a result of streaking effects. It is concluded that there is no hexagonal phase in the Si nanowires and the Si thin films presented in this work.

Combining precession electron diffraction data with X-ray powder diffraction data to facilitate structure solution

Xie, D. — 2008-12-01

Information derived from precession electron diffraction (PED) patterns can be used to advantage in combination with high-resolution X-ray powder diffraction data to solve crystal structures that resist solution from X-ray data alone. PED data have been exploited in two different ways for this purpose: (1) to identify weak reflections and (2) to estimate the phases of the reflections in the projection. The former is used to improve the partitioning of the reflection intensities within an overlap group and the latter to provide some starting phases for structure determination. The information was incorporated into a powder charge-flipping algorithm for structure solution. The approaches were first developed using data for the moderately complex zeolite ZSM-5, and then tested on TNU-9, one of the two most complex zeolites known. In both cases, including PED data from just a few projections facilitated structure solution significantly.

A tutorial for learning and teaching macromolecular crystallography

Faust, A. — 2008-12-01

Five experiments have been designed to be used for teaching macromolecular crystallography. The three proteins used in this tutorial are all commercially available; they can be easily and reproducibly crystallized and mounted for diffraction data collection. For each of the five experiments the raw images and the processed data of a sample diffraction data set as well as the refined coordinates and phases are provided for teaching the steps of data processing and structure determination.

Microstrain and grain-size analysis from diffraction peak width and graphical derivation of high-pressure thermomechanics

Zhao, Y. — 2008-12-01

An analytical method is presented for deriving the thermomechanical properties of polycrystalline materials under high-pressure (P) and high-temperature (T) conditions. This method deals with non-uniform stress among heterogeneous crystal grains and surface strain in nanocrystalline materials by examining peak-width variation under different P–T conditions. Because the method deals directly with lattice d spacing and local deformation caused by stress, it can be applied to process any diffraction profile, independent of detection mode. In addition, a correction routine is developed using diffraction elastic ratios to deal with severe surface strain and/or strain anisotropy effects related to nano-scale grain sizes, so that significant data scatter can be reduced in a physically meaningful way. Graphical illustration of the resultant microstrain analysis can identify micro/local yields at the grain-to-grain interactions resulting from high stress concentration, and macro/bulk yield of the plastic deformation over the entire sample. This simple and straightforward approach is capable of revealing the corresponding micro and/or macro yield stresses, grain crushing or growth, work hardening or softening, and thermal relaxation under high-P–T conditions, as well as the intrinsic residual strain and/or surface strain in the polycrystalline bulk. In addition, this approach allows the instrumental contribution to be illustrated and subtracted in a straightforward manner, thus avoiding the potential complexities and errors resulting from instrument correction. Applications of the method are demonstrated by studies of α-SiC (6H, moissanite) and of micro- and nanocrystalline nickel by synchrotron X-ray and time-of-flight neutron diffraction.

X-ray tomographic reconstruction of macromolecular samples

Brockhauser, S. — 2008-12-01

The anomalous scattering properties of innate sulfur for proteins and phosphorus for DNA and RNA can be used to solve the phase problem in macromolecular crystallography (MX) via the single-wavelength anomalous dispersion method (SAD). However, this method, which is carried out at longer X-ray wavelengths (1.5–2.5 Å), is still not a routine tool in MX. The increased absorption from both air and sample associated with the use of longer X-ray wavelengths presents a key difficulty. The absorption can be corrected for through empirical algorithms, provided truly redundant data are available. Unfortunately, weakly diffracting macromolecular crystals suffer from radiation damage, resulting in a dose-dependent non-isomorphism which violates the assumption upon which these empirical algorithms are based. In this report, X-ray microtomography is used to reconstruct the three-dimensional shapes of vitrified macromolecular crystals including the surrounding solvent and sample holder. The setup can be integrated within an MX beamline environment and exploits both absorption and phase contrast. The dose needed for the tomographic measurements could be low enough to allow the technique to be used for crystal integrity characterization and alignment. X-ray tomography has some major benefits compared with the optical-light-based crystal alignment protocols currently used.

Control of the rate of evaporation in protein crystallization by the `microbatch under oil' method

Brumshtein, B. — 2008-10-01

Microbatch crystallization under oil is a powerful procedure for obtaining protein crystals. Using this method, aqueous protein solutions are dispensed under liquid oil, and water evaporates through the layer of oil, with a concomitant increase in the concentrations of both protein and precipitant until the nucleation point is reached. A technique is presented for regulating the rate of water evaporation, which permits fine tuning of the crystallization conditions as well as preventing complete desiccation of the drops in the microbatch crystallization trays.

Study of the effect of nano-sized precipitates on the mechanical properties of boron-added low-carbon steels by neutron scattering techniques

Seong, B.S. — 2008-10-01

Small-angle neutron scattering (SANS) and neutron powder diffraction (ND) techniques were used to study quantitatively the effect of nano-sized precipitates and boron addition on the mechanical properties of low-carbon steels. SANS was used to evaluate nano-sized precipitates, smaller than about 600 Å in diameter, and ND was used to determine the weight fraction of the cementite precipitates. Fine core–shell structured spherical precipitates with an average radius of ~50 Å, such as MnS and/or CuS, surrounded by BN layers were observed in the boron-added (BA) low-carbon steels; fine spherical precipitates with an average radius of ~48 Å were mainly observed in the boron-free (BF) low-carbon steels. In the BA steels, the number of boron precipitates, such as BN, Fe3(C,B) and MnS, surrounded by BN layers increased drastically at higher hot-rolling temperatures. The volume fraction of the fine precipitates of the BA steels was higher than that of the BF steels; this difference is related to the rapid growth of the BN layers on the MnS and CuS precipitates. Boron addition to low-carbon steels resulted in a reduction in strength and an improvement in elongation; this behaviour is related to the reduction of the solute carbon and the nitrogen contents in the ferrite matrix caused by the precipitation of BN, as well by the increase in the volume fraction of the cementites.

Finding crystal structures from few diffraction data by a combination of a random search with genetic algorithms

Immirzi, A. — 2008-08-01

A new procedure for performing structural analysis of crystalline materials from diffraction data, using internal coordinates, is described. For starting information only unit-cell content, space group, chemical formula, molecular connectivity and a limited amount of diffraction data are required. After first selecting a number of solutions using a Monte Carlo approach with severe filters, which reject the most unrealistic solutions, genetic algorithms (crossover and mutations) are applied. In fact, the initial selection step alone is, frequently, a powerful tool for discovering structures, without recourse to the genetic algorithms. The procedure, while suffering from the limitation that connectivity must be known, is effective in cases where direct methods are not applicable because the diffraction data are scarce, are limited to low diffraction angles or are missing in specific portions of the reciprocal space. The main features of the algorithm are described and examples of validation given. The routines are now available as part of the freely distributed general-purpose program TRY. The program is available on the Web at http://www.theochem.unisa.it/try.html.

Point-focusing monochromator crystal realized by hot plastic deformation of a Ge wafer

Okuda, H. — 2008-08-01

Pre-polished Ge(111) single-crystal wafers were deformed just below the melting temperature to prepare point-focusing Johansson monochromator crystals. The (111) lattice plane had curvature 2R in the focusing plane and R perpendicular to it, with a hemispherical inner surface with a radius of R = 600 mm. By using Cu Kα radiation, the diverging X-ray beam was focused onto a small spot.

X-ray diffraction by polycrystalline materials. By René Guinebretière. Pp. 351. London: ISTE, 2007. Price (hardcover) EUR 124.83. ISBN 978-1905209217.

Chateigner, D. — 2008-08-01

A toolkit for publishing enhanced figures

McMahon, B. — 2008-08-01

An editing toolkit has been developed to allow authors to create enhanced interactive figures for publication in crystallography journals. The visualization engine is Jmol, a Java program that can be manipulated as an applet in a web browser. The toolkit provides user-friendly widgets to manipulate the graphics state of Jmol, and persistent storage of graphics state, scripts and associated data files.

VCIF2: extended CIF validation software

Todorov, G. — 2008-08-01

Recent revisions to the CIF standard, the growing number of dictionaries and the critical role played by CIF in the IUCr publication process led the IUCr to fund a two-year project to upgrade portions of the existing CIF software base to support longer lines and more rigorous validation of CIFs against multiple layered dictionaries. A database-based approach to validation to ensure compliance with data-range and enumeration specifications, to ensure compliance with parent–child relationships, and to detect missing and duplicated tags is presented here. This approach to validation is being extended to support the handling of binary synchrotron imgCIF data.

Of crystals, structure factors and diffraction images

Jovine, L. — 2008-06-01

It is suggested that it would be useful if raw X-ray diffraction images could be included in data depositions with the Protein Data Bank.

Determination of absolute structure using Bayesian statistics on Bijvoet differences

Hooft, R.W.W. — 2008-02-01

A new probabilistic approach is introduced for the determination of the absolute structure of a compound which is known to be enantiopure based on Bijvoet-pair intensity differences. The new method provides relative probabilities for different models of the chiral composition of the structure. The outcome of this type of analysis can also be cast in the form of a new value, along with associated standard uncertainty, that resembles the value of the well known Flack x parameter. The standard uncertainty we obtain is often about half of the standard uncertainty in the value of the Flack x parameter. The proposed formalism is suited in particular to absolute configuration determination from diffraction data of biologically active (pharmaceutical) compounds where the strongest resonant scattering signal often comes from oxygen. It is shown that a reliable absolute configuration assignment in such cases can be made on the basis of Cu Kα data, and in some cases even with carefully measured Mo Kα data.

GenOVa: a computer program to generate orientational variants

Cayron, C. — 2007-12-01

A computer program called GenOVa, written in Python, calculates the orientational variants, the operators (special types of misorientations between variants) and the composition table associated with a groupoid structure. The variants can be represented by three-dimensional shapes or by pole figures.

ARPGE: a computer program to automatically reconstruct the parent grains from electron backscatter diffraction data

Cayron, C. — 2007-12-01

A computer program called ARPGE written in Python uses the theoretical results generated by the computer program GenOVa to automatically reconstruct the parent grains from electron backscatter diffraction data obtained on phase transition materials with or without residual parent phase. The misorientations between daughter grains are identified with operators, the daughter grains are identified with indexed variants, the orientations of the parent grains are determined, and some statistics on the variants and operators are established. Some examples with martensitic transformations in iron and titanium alloys were treated. Variant selection phenomena were revealed.

Illustrated Fourier transforms for crystallography

Aubert, E. — 2007-12-01

Concepts such as Fourier transformation, convolution and resolution that are required to understand crystallography are illustrated through visual examples. These concepts can be explained pedagogically in a very direct way using the DigitalMicrograph software from Gatan Inc. (http://www.gatan.com/imaging/downloads.php), originally intended for electron microscopy data collection and analysis, and practical exercises developed around this tool can be used in teaching crystallography.

Meeting report of the BCA 25th Annual Meeting held at the University of Kent in Canterbury, UK, 16–19 April 2007

Helliwell, J.R. — 2007-08-01

A report on the BCA 25th Annual Meeting held at the University of Kent in Canterbury, UK, 16–19 April 2007.

Phaser crystallographic software

McCoy, A.J. — 2007-08-01

Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

Personal X-ray reflections. By U. W. Arndt. Pp. 177. Twickenham: Athena Press, 2006. Price GBP 6.99, USD 11.95. ISBN 1-84401-694-3.

Helliwell, J.R. — 2007-06-01

Vesicles as reactors of nanoparticles: an anomalous small-angle X-ray scattering study of the domains rich in copper ions

Bóta, A. — 2007-04-21

The formation of copper hydroxide and copper oxide particles in the gaps among the stacks of multilamellar vesicles is described, illustrating a new pathway in the preparation of nanometre-scale particles. The in situ structural characterization of both the solid particles and the vesicles as a reaction medium was performed in the initial and final states of the process by using anomalous small-angle X-ray scattering (ASAXS) and freeze-fracture methods. The ASAXS method provides a description of the particle-size distribution of the copper nanoparticles, in spite of the fact that they are present in low concentration. This method allows the particle formation and growth to be monitored throughout the whole time range of the synthesis.

Structural formation and many-body effect of concentrated dendrimer solutions by computer simulations

Terao, T. — 2007-04-21

Coarse-grained molecular dynamics simulations have been performed in order to study charged dendrimers in an aqueous solution. The structure factor, counterion distribution and effective interaction between molecules are clarified numerically. In particular, the many-body interactions in a triplet system are investigated, which is of importance in concentrated systems. These results shed new light on the analysis of recent small-angle X-ray and neutron scattering experiments on dendrimer solutions.

Salt-concentration dependence of the structure and form factors for the wormlike micelle made from a dual surfactant in aqueous solutions

Eguchi, K. — 2007-04-21

Small-angle X-ray scattering (SAXS) from dual-surfactant aqueous solutions made from sodium lauryl ether sulfate and coconut fatty acid amido propyl betaine was systematically measured as a function of the net sodium cation concentration, [Na+]*, and the surfactant concentration, CD. The SAXS intensity [I(q)] was normalized to CD and the resultant I(q)/CD was extrapolated to CD = 0 to give a form factor P(q) for each [Na+]* [where q = 4πsin(θ/2)/λ is the magnitude of the scattering vector, λ is the wavelength and 2θ is the scattering angle]. The low-q behaviour of P(q) was consistent with long rigid cylinders. The middle- and high-q profiles fitted well with a core–shell cylinder model for all [Na+]*. The core and total radii (Rc and Rs) did not depend on [Na+]* at all: Rc = 1.2 ± 0.05 and Rs = 3.1 ± 0.05 nm for [Na+]* = 0.42–1.5 mol l−1, indicating that the salt concentration changes did not induce any structural changes and re-assembling of the surfactants comprising the micelles. This fact is in contrast to the rheological behaviour where the relaxation mode strongly depends on [Na+]*. The structure factor [S(q)] was obtained by dividing I(q)/CD by P(q) for each CD and the mean distance (dm) between the micelles was obtained from the first maximum of S(q) versus q plots. The dm value decreased with increasing CD and [Na+]*, which is in good agreement with the theoretical prediction and experimental results for charged wormlike micelle solutions.

X-ray fluorescence correlation spectroscopy – a tool to study element-specific dynamics

Leupold, O. — 2007-04-21

We have explored the feasibility of X-ray fluorescence correlation spectroscopy for studying the dynamics of colloidal particles in solution. We measured suspensions of Au nanoparticles from 5 to 150 nm diameter in water/glycerol mixtures of various compositions. Time-averaged sample properties were traced via small-angle X-ray scattering. The contrast of the measured time-correlation functions scales as expected with the particle concentration in the sample. The time constants for translational diffusion and sedimentation in water/glycerol mixtures follow only qualitatively the expected behaviour.

Focusing and polarized neutron small-angle scattering spectrometer (SANS-J-II). The challenge of observation over length scales from an ångström to a micrometre

Koizumi, S. — 2007-04-21

SANS-J (a pinhole small-angle neutron scattering spectrometer at research reactor JRR3, Tokai, Japan) was reconstructed as a focusing and polarized neutron small-angle scattering spectrometer (SANS-J-II). By employing focusing lenses of a biconcave MgF2 crystal or of a sextupole permanent magnet and a high-resolution photomultiplier, the minimum accessible magnitude of the scattering vector qmin was improved from 3 × 10−3 Å−1 to an ultra-small-angle scattering (USAS) of 3 × 10−4 Å−1. Compared with a Bonse–Hart double-crystal method, the advantages of focusing USAS are the efficient detection of anisotropic USAS with an area detector, an improvement in q resolution Δq/q at conventional magnitudes of the scattering vector q ~ 10−3 Å−1 and a gain in neutron flux in the conventional q region of q ~ 10−3 Å−1.

Shear-induced structural transition in the lamellar phase of the C16E7/D2O system. Time evolution of small-angle neutron scattering at a constant shear rate

Miyazaki, K. — 2007-04-21

The time evolution of small-angle neutron scattering is measured for the lamellar phase of a nonionic surfactant C16H33(OC2H4)7OH (C16E7) in D2O at 48 wt% at 343 K under shear flow. At the shear rates of 0.3, 1 and 3 s−1, a new diffraction peak appears at higher q [where q = (4π/λ)sin θ, and λ and 2θ are the wavelength of the neutron beam and the scattering angle, respectively] about 1–2 h after applying shear flow and coexists with the initial diffraction peak. The coexistence of two peaks continues even after 5 h at 0.3 s−1 whereas at 1 and 3 s−1 the peak at lower q disappears after about 3 h. These results indicate that the repeat distance decreases discontinuously and so suggest some sort of transition. A plot of the repeat distance after 5 h versus shear rate shows a minimum at 1 s−1, which is in good agreement with our previous results obtained by increasing the shear rate stepwise.

Effect of lithium trifluoromethanesulfonate on the phase diagram of a liquid-crystalline amphiphilic diblock copolymer

Yamada, T. — 2007-04-21

Phase transitions and nanometre-scale ordered structures of a binary system of a liquid-crystalline amphiphilic diblock copolymer, poly(ethylene oxide)-b-poly{11-[4-(4-butylphenylazo)phenoxy]undecyl methacrylate} [PEOm-b-PMA(Az)n, where m and n are the degrees of polymerization of the PEO and PMA(Az) domains, respectively], and lithium trifluoromethanesulfonate (LiCF3SO3) were investigated by differential scanning calorimetry and small-angle X-ray scattering (SAXS). PEO114-b-PMA(Az)51 formed a highly ordered hexagonally packed PEO cylinder structure in the temperature range below 393 K and transformed to a body-centred-cubic structure in the isotropic state above 393 K. The PEO114-b-PMA(Az)51/LiCF3SO3 systems with various LiCF3SO3 concentrations (molar ratio 0 < LiCF3SO3/EO = fLi < 1) formed the hexagonally packed cylinder structure at room temperature. From the effects of LiCF3SO3 concentration on the phase transitions, the size and the order of the hexagonally packed cylinder structure, it was found that PEO114-b-PMA(Az)51 and LiCF3SO3 formed a complex efficiently at a molar equivalent of three ethylene oxide repeating units per LiCF3SO3 unit. The ordering of the hexagonally packed cylinder structure decreased with increasing LiCF3SO3 concentration and the radius of the PEO cylinder evaluated by SAXS profile fitting increased from 2.7 to 8.3 nm. For the PEO114-b-PMA(Az)51/LiCF3SO3 system with fLi = 1, the hexagonally packed cylinder structure remained even in the isotropic state because the PEO volume fraction (φPEO) increased from φPEO = 0.06 (fLi = 0) to φPEO = 0.23 (fLi = 1) on the formation of the LiCF3SO3/PEO complex.

Evaluation of multiple small-angle neutron scattering including magnetic interactions

Šaroun, J. — 2007-04-21

Analytical formulae describing multiple small-angle neutron scattering in ferromagnetic materials are derived from transport equations. The derivation is based on Molière's theory of multiple small-angle scattering assuming that the mean free path of the neutrons is large compared to the size of the scatterers. In addition to the formalism developed earlier for nuclear scattering, the new formulation takes into account the spin dependence of the scattering cross section and spin flips caused by subsequent scattering events. This leads to an anomalous distribution of scattering intensity and polarization, as demonstrated by examples of model calculations and Monte Carlo simulations. In particular, multiple scattering of polarized neutrons can lead to either smoothing or sharpening of the scattered beam anisotropy depending on the polarization of the primary beam and the nuclear and magnetic contrasts of the scatterers. The presented theory has been implemented in the data-fitting program SASProFit suitable for both the modelling of multiple scattering effects and the analysis of experimental data.

X-ray studies of the self-organized structure formed by 1,2-bis(4'-n-alkoxybenzoyl)hydrazine (BABH-n) homologues. 1. Ia3d-gyroid structure

Kutsumizu, S. — 2007-04-21

The cubic (Cub) phase structure of a thermotropic mesogen 1,2-bis(4′-n-alkoxybenzoyl)hydrazine (BABH-n, where n is the number of C atoms in the aliphatic tail) was examined by small-angle X-ray scattering. The BABH-n system exhibits two types of Cub phases, Ia3d type and Im3m type. In the phase diagram as a function of the tail length (n) the Im3m-Cub phase region (n = 13–16) was sandwiched by two Ia3d-Cub phase regions with n < 13 and n > 16. On the basis of the triply periodic minimal surface (TPMS) picture, the Ia3d and Im3m structures are described by the gyroid (G) and doubled-P (PP) surfaces, respectively. In this paper we focused attention on the internal structure of the Ia3d-Cub phase at the molecular level. By examining how the relative intensity of the 220 reflection with respect to the 211 reference peak varies with n, we have successfully determined the position of the aliphatic tails, which are located on the G-TPMSs. As far as we know, this is the first approach to clarifying the internal structure of the thermotropic Ia3d-Cub phase. The usefulness of the systematic studies with respect to the tail length n has also been demonstrated.

Operator-assisted harvesting of protein crystals using a universal micromanipulation robot

Viola, R. — 2007-06-01

High-throughput crystallography has reached a level of automation where complete computer-assisted robotic crystallization pipelines are capable of cocktail preparation, crystallization plate setup, and inspection and interpretation of results. While mounting of crystal pins, data collection and structure solution are highly automated, crystal harvesting and cryocooling remain formidable challenges towards full automation. To address the final frontier in achieving fully automated high-throughput crystallography, the prototype of an anthropomorphic six-axis universal micromanipulation robot (UMR) has been designed and tested; this UMR is capable of operator-assisted harvesting and cryoquenching of protein crystals as small as 10 µm from a variety of 96-well plates. The UMR is equipped with a versatile tool exchanger providing full operational flexibility. Trypsin crystals harvested and cryoquenched using the UMR have yielded a 1.5 Å structure demonstrating the feasibility of robotic protein crystal harvesting.

Hierarchical structure of niobate nanosheets in aqueous solution

Yamaguchi, D. — 2007-04-21

The hierarchical structure of an aqueous dispersion of niobate nanosheets was explored by using a combined method of ultra-small-angle and small-angle scattering of neutrons and X-rays. The concentration of the sheets studied was in the range where the dispersion exhibits a liquid-crystal phase as evidenced by observation between crossed polarizers in a previous report. The scattering data covered a wide q scale of more than four orders of magnitude [3 × 10−4 ≤ q ≤ 10 nm−1, where q = (4π/λ)sin(θ/2), λ and θ being the wavelength of the incident beam and the scattering angle, respectively], corresponding to the length scale l = 2π/q from ~1 nm to ~20 µm. The scattering analyses provided information on the hierarchical structural elements including: (i) single nanosheets as a structure element (hierarchy I), (ii) parallel stacks of the sheets (hierarchy II), and (iii) spatial arrangements of the stacks (hierarchy III), in order of increasing length scale. Hierarchy II is closely related to the liquid-crystal nature of the dispersion in which the spacing and the persistence length, normal and parallel to the stack surface, respectively, were disclosed. Hierarchy III gives rise to the low-q upturn in the scattering profile, which may be characterized by mass-fractal-like power-law scattering behavior. This finding is a surprise from the viewpoint of the liquid-crystal nature of the dispersion, a possible model of which is proposed in the text.

Characterization of two-dimensional ultra-small-angle X-ray scattering apparatus for application to rubber filled with spherical silica under elongation

Shinohara, Y. — 2007-04-21

Two-dimensional ultra-small-angle X-ray scattering (2D-USAXS) apparatus at SPring-8 has been characterized. 2D-USAXS is a promising tool to study the structural change of the hierachical aggregate structure of fillers such as carbon black and silica particles in rubber. The aggregate structure of fillers is key to understanding the reinforcement effects which fillers show in rubber. We have applied 2D-USAXS to rubber filled with spherical silica particles and proved it to be a powerful technique.

Study on two-dimensional small-angle X-ray scattering of in situ silica filled nanocomposite elastomer during deformation

Ikeda, Y. — 2007-04-21

Morphological change of in situ generated silica particles was investigated by a time-resolved two-dimensional small-angle X-ray scattering technique and a simultaneous tensile measurement. The in situ silica particles with diameter ca 34 nm were homogeneously dispersed in a rubbery matrix and the morphological change of the particles was followed up to the elongation ratio α = 2 during stretching and from α = 2.5 during retracting. The observed two-dimensional small-angle X-ray scattering patterns agreed with the simulation results by Rharbi et al. [Europhys. Lett. (1999), 46, 472–478] where a shear displacement model was proposed for the deformation mode of their soft nanocomposite.

Lamellar crystal thickness transition of melt-crystallized isotactic polybutene-1 observed by small-angle X-ray scattering

Yamashita, M. — 2007-04-21

The first-order long period L1, the second-order long period L2 and lamellar crystal thickness lc of isotactic polybutene-1 have been investigated for crystallization in the melt over a wide range (313.2 to 363.2 K) of crystallization temperatures by small-angle X-ray scattering experiments and density measurements. The long period L1 shows a single linear dependence on inverse supercooling. The crystal thickness lc, however, demonstrates two linear dependences on inverse supercooling and a transition from one dependence to the other has been observed around 338.2 K, where lc becomes comparable with the radius of gyration Rg of the samples.

Surface free energies of isotactic polybutene-1 tetragonal and trigonal crystals: the role of conformational entropy of side chains

Yamashita, M. — 2007-04-21

Lateral and end surface free energies of melt-crystallized isotactic polybutene-1 (it-PB1) trigonal and tetragonal crystals have been determined by small-angle X-ray scattering and in situ observation of the crystal growth kinetics. The lateral surface free energy σ of the trigonal phase is about seven times as large as the value σHoff calculated according to Hoffman's equation [Hoffman (1992). Polymer, 33, 2643–2644], while that of the tetragonal phase is roughly in agreement with the estimation. The discrepancy between the values of σ and σHoff for the trigonal phase can be attributed to the loss of conformational entropy of the ethyl side chains of it-PB1.

Phase behavior of platelet-shaped nanosilicate colloids in saline solutions – a small-angle X-ray scattering study

Fonseca, D.M. — 2007-04-21

A study of polydisperse suspensions of fluorohectorite clay in saline solutions is presented. The suspended clay colloids consist of stacks of nanosilicate sheets several tenths of a nanometre thick. They are polydisperse both with respect to the number of stacked nanolayers and with respect to their extension along the sheets. Due to this polydispersity, a spontaneous gravity-induced vertical segregation occurs in the sample tubes and results in the presence of up to four different phases on top of each other. Precise characterization of the phase diagram of the samples as a function of salt concentration and vertical position in the tubes, based on small-angle X-ray scattering data, is presented. The vertical positions of the phase boundaries were monitored by analyzing the eccentricity of elliptic fits to iso-intensity cuts of the scattering images. The intensity profiles along the two principal directions of scattering display two power-law behaviors with a smooth transition between them and show the absence of positional order in all phases.

Repulsive interlamellar interaction induced by addition of colloidal particles

Suganuma, Y. — 2007-04-21

The effects of colloidal particles confined between lamellar membrane slits on interlamellar interactions have been investigated by small-angle neutron scattering. On addition of colloidal particles to a lamellar phase composed of a non-ionic surfactant, the first lamellar peak becomes sharper and higher-order peaks appear. Thus the colloidal particles suppress undulation fluctuations of lamellar membranes by their steric hindrance, which results in a repulsive interlamellar interaction. As the interlamellar distance decreases, the position of the Bragg peak shifts towards higher q [where q is the magnitude of scattering vector, given by q = (4\pi/\lambda)\sin\theta, where 2\theta is the scattering angle and λ is the wavelength] and the peak intensity weakens. This tendency is completely opposite to the behavior of non-ionic surfactant lamellar phases, where the interlamellar interaction is governed by the Helfrich interaction. A phenomenological free-energy model is proposed based on the restriction of membrane fluctuations by colloidal particles. This model describes the experimental results well.

Solution structure of Ca2+/calmodulin complexed with a lentivirus lytic peptide 1 reveals a novel mode of molecular recognition

Izumi, Y. — 2007-04-21

Small-angle X-ray scattering was used to analyze the interaction of Ca2+/calmodulin (CaM) with a lentivirus lytic peptide 1 (LLP1) derived from the cytoplasmic tail of HIV-1 transmembrane glycoprotein. The synthetic peptide homologues of LLP1 were selected from three species of the glycoprotein: ENV_HV1A2, ENV_HV1B1 and ENV_HV1H2. Ca2+/CaM binds LLP1 with the truncation of three or ten residues and adopts almost the same globular structure as that of the complex with a peptide from myosin light chain kinase (MLCK), indicating that the Ca2+/CaM-binding site locates on the shorter sequence. Moreover, Ca2+/CaM binds a peptide with the opposite sequence and adopts almost the same globular structure as that in the original sequence. Taken together, the results provide evidence that LLP1 can bind to the N- and C-terminal lobes of CaM with a polarity opposite to that observed for the CaM–MLCK complex and the binding mode of Ca2+/CaM molecular recognition is well preserved despite the sequence variation in the three species, suggesting that this region of the transmembrane glycoprotein is important to viral replication.

Living anionic polymerization of methyl methacrylate controlled by metal-free phosphazene catalyst as observed by small-angle neutron scattering, gel-permeation chromatography and UV–visible spectroscopy

Miyamoto, N. — 2007-04-21

Phosphazene (PZN) catalyst, PZN catalyst coexisting with a co-catalyst 1-hydroxycyclohexyl phenyl ketone (Irgacure 184; IRG) and polymethylmethacrylate (PMMA) (prepared by catalytic living anionic polymerization using the PZN catalyst and IRG) have been observed for the first time by small-angle neutron scattering (SANS) and UV–visible spectroscopy to elucidate the aggregation behavior of the PZN molecules themselves and the state of living chain ends in a living polymer solution. PZN catalyst in deuterated tetrahydrofuran (thf-d8) showed SANS curves fitted by a form factor for a sphere whose radius Rs is larger (1.4–1.6 nm) than a single PZN molecule (0.65 nm), indicating formation of PZN aggregates in thf-d8. In a nonpolar solvent, benzene-d6, Rs was even larger (3.1 nm), indicating formation of larger aggregates. By adding IRG to PZN solution, an excess scattering appeared in the SANS profile and a strong band emerged in the UV–visible spectrum. This result indicates strong interaction of IRG with PZN not only on a molecular scale but also on a mesoscopic scale. The SANS profile from the living polymer solution in thf-d8 was observed to be fitted by the sum of the profile for the aggregated PZN/IRG complex and that for Gaussian chains of PMMA. The molecular weight of the PMMA determined by SANS, 2100 g mol−1, was in agreement with that estimated from gel-permeation chromatography, indicating that the anionic living chain ends and their counter ions (PZN) are dissociated in thf-d8; thus, the chains are not associated into multiple-ion pairs.

Study of ferrite ferrofluids by small-angle scattering of polarized neutrons

Bonini, M. — 2007-04-21

Nanoparticles consisting of a magnetic core (Fe3O4, CoFe2O4 and CuFe2O4) and a hydrophobic shell were prepared by chemical co-precipitation of the inorganic cores and by subsequently modifying the surface with dodecanoic acid. The nanoparticles were then dispersed in cyclohexane to form stable ferrofluids. These dispersions were investigated by small-angle scattering of polarized neutrons and the data were interpreted according to a `pearl-necklace' model, opportunely modified to account for the core–shell structure of the particles. Results of the fitting show that the particles consist of a magnetic core with a mean radius of 40–50 Å and an organic shell with a thickness of 7–8 Å. These nanoparticles assemble in fractal aggregates when a magnetic field is applied.

Biological small-angle X-ray scattering facility at the Stanford Synchrotron Radiation Laboratory

Smolsky, I.L. — 2007-04-21

Beamline 4-2 at the Stanford Synchrotron Radiation Laboratory is a small-angle X-ray scattering/diffraction facility dedicated to structural studies on mostly noncrystalline biological systems. The instrument consists of a pinhole camera, which covers the magnitude of the scattering vector Q in the range 0.004–1.3 Å−1 [Q = (4π/λ)sin θ, where θ and λ are one half of the scattering angle and the X-ray wavelength, respectively], and a Bonse–Hart geometry ultra-small-angle X-ray scattering setup for the Q range an order of magnitude smaller. The pinhole camera allows quick automated distance and detector selection among any combination of five distances and three position-sensitive detectors. The double-crystal monochromator can have either Si 111 crystals or a pair of synthetic multilayer diffractive elements for higher flux applications. We have adopted a suite of software originally developed for macromolecular crystallography for integrated beamline control as well as static and slow time-resolved small-angle scattering data collection. This article outlines recent technological developments and specialized instrumentation for conducting noncrystalline scattering experiments in structural biology at improved time and spatial resolutions.

Small-angle light and X-ray scattering measurements of a protein–oligosaccharide complex mucin in solution

Watanabe, Y. — 2007-04-21

The molecular assembly and the chain conformation of intact bovine submaxillary mucin (BSM) in solution over wide-ranging concentrations were characterized by using low-angle laser light scattering and small-angle X-ray scattering (SAXS) methods. The specific refractive index increment of BSM was estimated to be 0.152 ml g−1 and was used to determine the molecular weight of BSM by low-angle laser light scattering photometry combined with high-performance gel chromatography. The total molecular weight of BSM was 55 million and the molecular weight of the main fractionated components was about 2 million. Fractal analysis of the SAXS data revealed that the intact BSM molecule is a chain with excluded volume (fractal dimension 1.67) at concentrations of 1.4 and 3.6 mg ml−1 and a chain with a Gaussian chain character (fractal dimension 2) at concentrations of 7.2–15 mg ml−1. Moreover, the Kratky plots of the SAXS data showed that the chain conformation of BSM molecules is a Gaussian (unfolded) structure in solution. The estimated cross-sectional radius of gyration value lay in the range 0.65–0.76 nm, which is reasonable for a long thin shape.

New two-dimensional data treatment software for small-angle scattering

Pépy, G. — 2007-04-21

A new program is presented which performs data treatment in one, two or three dimensions. While one-dimensional data treatment can be performed easily by many programs (canSAS, EMBL, ISIS, ILL, NIST), few deal efficiently with more dimensions. Indeed, specific attention has to be paid to the selection of the relevant data. Their display and models are relatively complex. This new program has been developed according to the needs of small-angle scattering users, but is not limited to these fields. Its original purpose was to model forward anisotropic scattering and diffuse scattering typically produced by large structures such as polymers, aggregates, self-assembly systems or micellar solutions. It is also suited to modelling Bragg scattering. With time, many filter configurations (rectangles or sectors, with possible symmetries and display along various coordinates) and many model functions (centred or not, possibly with cofactors, with Cartesian, polar, or three-dimensional coordinates) have been added. Models are fitted by the steepest descent model with χ2 as the minimization function. The software is written in Fortran with the PGPLOT graphics package. It runs with the Windows operating system.

Multiple-length-scale small-angle X-ray scattering analysis on maghemite nanocomposites

Millan, A. — 2007-04-21

Small-angle X-ray scattering (SAXS) analysis has been performed on maghemite–poly(4-vinylpyridine) nanocomposites prepared by in situ precipitation from iron–polymer coordination compounds. According to electron microscopy observations, the nanocomposites contain isolated spherical particles with a narrow size distribution, uniformly distributed throughout the polymer matrix. The scattering intensity of nanocomposites has relevant contributions from both the polymer and the nanocomposites, showing features characteristic of multiscale structured systems, namely two power laws and a Guinier regime. The data have been analysed in terms of Beaucage's unified approach and it is found that the maghemite particle size increases with the iron/polymer weight ratio used in the preparation of the nanocomposites. SAXS curves also feature a bump that was analysed as arising from a second particle population or from interactions. Magnetization and transmission electron microscopy results give arguments favouring the latter interpretation. It is found that the maghemite particle sizes vary linearly with the iron weight ratio used in the preparation of the nanocomposites.

Initial process of amyloid formation of apomyoglobin and effect of glycosphingolipid GM1

Onai, T. — 2007-04-21

Using small-angle and wide-angle X-ray scattering techniques it has been possible to clarify the helix-to-sheet (cross-β) transition and the stacking process of the cross-β sheet of apomyoglobin as a model for amyloid. The present results indicate that the cross-β formation and the pleated sheet stacking start concurrently and that the stacking continues progressively after the saturation of the cross-β formation. The effect of glycosphingolipids on the above processes has also been studied. At high molar ratio of glycosphingolipid to apomyoglobin the growth of the amyloid is suppressed.

Small-angle X-ray and small-angle neutron scattering investigations of colloidal dispersions of magnetic nanoparticles and clay nanoplatelets

Paula, F.L.O. — 2007-04-21

We investigated mixed colloidal dispersions of clay platelets and magnetic nanoparticles using small-angle X-ray and neutron scattering. Our results show that the contribution to the scattering is essentially due to the magnetic nanoparticles. The scattering intensities are proportional to the concentration of magnetic particles, indicating that from the scattering point of view the sample is a colloidal dispersion of non-interacting magnetic objects, although the laponite and magnetic particles clearly interact when the sample textures are observed in an optical microscope. The visually observed phase separation may be characterized as a liquid–gas transition.

Measurement of self-diffusion constant with two-dimensional X-ray photon correlation spectroscopy

Robert, A. — 2007-04-21

The X-ray photon correlation spectroscopy technique probes the slow dynamics of disordered materials, overcoming the limitations of using photon correlation spectroscopy with coherent visible light. It extends the accessible range of the modulus of the scattering vector to short wavelength density fluctuations and is not sensitive to multiple scattering. We measure here experimentally the short-time self-diffusion coefficient D_{\rm S} of a charge-stabilized colloidal dispersion. It is in contradiction with theoretical models including many-body hydrodynamic interactions.

The dynamic behavior of magnetic colloids in suspension

Autenrieth, T. — 2007-04-21

The dynamic behavior of magnetic colloidal particles in suspension is investigated. The particles of the core–shell colloid consist of a cobalt ferrite core embedded in a silica shell and are stabilized by surface charges. As the suspension is strongly opaque to visible light, it can not be probed by dynamic light scattering techniques as a result of strong multiple scattering as well as absorption effects. Therefore, the static and dynamic behavior is probed with small-angle X-ray scattering and X-ray photon correlation spectroscopy (XPCS), respectively. Using XPCS, we are able to study the diffusion coefficient of an opaque colloidal system as a function of the scattering vector. In this paper, we report on the behavior of the colloidal system in the absence of an external magnetic field, meaning that the magnetic moments of the particles are oriented randomly. We find no evidence for magnetic interactions in the static data, while the dynamic XPCS data deviate very significantly from the predictions of model calculations.

Structural characterization of N-lignoceroyl (C24:0) sphingomyelin bilayer membranes: a re-evaluation

Takahashi, H. — 2007-04-21

Sphingomyelin (SM) is a membrane lipid and plays important roles in signaling, protein trafficking, cell growth and death. The structure of the bilayer of a hydrated highly asymmetric SM, N-lignoceroyl (C24:0) SM, has been investigated with X-ray diffraction (XRD), simultaneous small-angle X-ray scattering (SAXS), wide-angle XRD and SAXS. At temperatures between two endothermic transitions of hydrated C24:0 SM bilayers, the C24:0 SM formed a ripple phase with the ripple periodicity of ~12–14 nm. At about three months incubation at 277 K, the formation of a stable phase with a short lamellar spacing of 5.62 nm was induced. Based upon the structures revealed by this study and the phase behavior, intermolecular interactions between C24:0 SM molecules in the bilayer membrane are discussed.

Mesoscopic structure of dry-pressed clay samples from small-angle X-ray scattering measurements

Méheust, Y. — 2007-04-21

Weakly hydrated samples of platelet-shaped nano-particles obtained by dry-pressing suspensions of the synthetic Na fluorohectorite clay are studied. The particles consist of stacks of several tens of 1 nm-thick nanosilicate platelets. They form a compound of quasi-two-dimensional particles whose average director is aligned with the direction of the uniaxial stress applied at dehydration. Small-angle X-ray scattering images from these samples are either isotropic or anisotropic, depending on the sample orientation with respect to the X-ray beam. From anisotropic images, changes in the scattering objects' orientation distribution probability (ODP) function are investigated as the temperature is lowered, thus triggering swelling of the individual particles by water intercalation. This is done, on the one hand, by inferring the width of the ODP function from the eccentricity of quasi-elliptic iso-intensity cuts of the small-angle scattering images, and, on the other hand, by obtaining the ODP function from azimuthal profiles of the images. The decays of the scattering intensity as a function of momentum transfer along the two principal directions of the images exhibit power law behaviors. A crossover scale between two power law regimes is observed on the profiles recorded along the horizontal axis; it corresponds to the typical pore size along the direction of the initially applied load. These results are compared with a previous study of similar systems.

Structural development of dynamically asymmetric polymer blends under uniaxial stretching

Takeno, H. — 2007-04-21

The time-resolved small-angle X-ray scattering technique was used to investigate the structural change during uniaxial stretching of dynamically asymmetric polymer blends irradiated by an electron beam. The concentration fluctuations were enhanced by stretching and became large in particular along the direction of deformation. In the early stages of the stretch-induced enhancement of concentration fluctuations, the growth rate of their q-Fourier mode was found to have a maximum at a certain value of q [= (4π/λ)sin(θ/2), where θ and λ are the scattering angle and the wavelength of the X-rays, respectively]. A dominant mode in the enhancement of concentration fluctuations exists in the initial stage, like the early stage of spinodal decomposition for fluid mixtures. The viscoelastic effects of the growth rate were taken into consideration, so that for blends irradiated by an electron beam, elastic effects are found to significantly suppress the growth rate of concentration fluctuations at small wavenumbers.

Chloride-ion concentration dependence of molecular dimension in the acid-denatured state of equine β-lactoglobulin

Yamada, Y. — 2007-04-21

The chloride-ion concentration dependence of the molecular dimension in the acid-denatured state of equine β-lactoglobulin (ELG) was investigated by small-angle X-ray scattering. In the presence of chloride ion, ELG has a globular and compact conformation (the A state). The molecular dimension of ELG increases little with decreasing chloride-ion concentration. A remarkable dependence was observed for a mutant protein in which both Cys66 and Cys160 were replaced with Ala (C66A/C160A). In the presence of chloride ion, C66A/C160A has a globular and compact conformation, like the wild type. In the absence of chloride ion, however, the molecular dimension and shape was close to that in the urea-unfolded state. Previously, we have shown that the helix content in the acid-denatured state increases with decreasing chloride-ion concentration [Yamada et al. (2006). Proteins Struct. Funct. Bioinf. 63, 595–602]. These results suggest that the secondary structure in the A state is mainly determined by non-local interactions. When they are absent in an expanded conformation, the local interactions become predominant and the amount of non-native α-helix increases.

Effect of cations on the structure of sodium bis(2-ethylhexyl)sulfosuccinate water-in-oil microemulsion

Kawai-Hirai, R. — 2007-04-21

We have characterized the structure of water/sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/isooctane water-in-oil microemulsion depending on the concentrations of monovalent and divalent cations (Na+, K+, Ca2+) in the water pool. We have found that the presence of salts affects the microemulsion structures differently at low and high water contents. Increasing the salt concentration suppresses the oligomerization of the microemulsions at low water content, whereas it reduces the microemulsion radius at high water content. The present results clearly indicate that not only electrostatic repulsion between AOT headgroups but also negative or positive hydration effects by salts dominate the structure and dynamics of AOT microemulsions, as suggested by a recent molecular dynamics simulation.

Time-resolved grazing-incidence small-angle X-ray scattering studies of lipid multibilayers with the insertion of amyloid peptide during the swelling process

Lin, J.-M. — 2007-04-21

The β-amyloid peptide (Aβ) (1–40) is one of the major components that form Alzheimer's amyloid deposits. Studies of the membrane insertion of amyloid showed that amyloid is surface active and can insert into lipid monolayers [Ji et al. (2002). Biochemistry (Moscow), 67, 1283–1288; Ege & Lee (2004). Biophys. J. 87, 1732–1740]. The interaction between the peptide and a lipid monolayer or bilayer is critical to the understanding of the formation of amyloid peptide deposits on the membrane. In this paper, we have studied the structural transition of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) multibilayers with the insertion of amyloid peptide 1–40 by grazing-incidence small-angle X-ray scattering at different bilayer hydration levels (changing the relatively humidity). We mixed the DPPC and amyloid peptide in an organic solvent at a 10 to 1 weight ratio, then cast it onto a silicon wafer to form the mixed lipid multibilayer film. In this study of the pure DPPC multibilayer film and the DPPC multibilayer film inserted with amyloid peptide, it was found that the hydration process was bimodal with a better-hydrated top layer and a less-hydrated bottom layer. The gel-to-ripple phase transition suffers a strong confinement effect due to the presence of the solid substrate. With the insertion of the amyloid peptide, the ripple phase of the membrane bilayers was suppressed at high humidity and the whole film can be swollen more uniformly at lower incubation time than the pure DPPC film supported on a silicon wafer. This means water vapor can penetrate more easily into the DPPC bilayers inserted with Aβ than into the pure DPPC bilayers. Amyloid peptides were found to form clusters in the bilayer and possess in-plane correlation. From analyzing the diffuse scattering around the Bragg peak in the lateral direction, the amyloid peptides are found to form clusters in the bilayer with a radius of about 9 nm. It is also estimated that the number of Aβ molecules in one cluster is about 12 and on average each Aβ molecule occupies an interface area of about 22 nm2. As the relative humidity exceeds about 94%, the Aβ clusters seem to develop an ordered structure with a spacing of about 300 Å.

Small-angle X-ray scattering investigation of water droplets in mist

Yano, Y.F. — 2007-04-21

Small-angle X-ray scattering measurements of water droplets in a mist were carried out using the BL15XU beamline at SPring-8. The diameter of the water droplets generated by ultrasonic atomization was found to be ≥ 50 nm and had no distribution in the range under 50 nm, as predicted. The study also showed how difficult it is to measure the small-angle scattering of low-density materials, such as liquid droplets in a mist.

Small-angle scattering investigations of magnesium hydride used as a hydrogen storage material

Pranzas, P.K. — 2007-04-21

In this work, high-energy ball-milled magnesium hydride samples used for hydrogen storage are investigated using small- and ultra-small-angle neutron scattering (SANS) as well as small-angle X-ray scattering (SAXS). Size distributions of inhomogeneities with dimensions from 10 Å up to more than 10 µm, corresponding to crystallite and particle sizes obtained by X-ray diffraction and electron microscopy, are determined as a function of milling time, milling tool material and added metal oxide catalysts in order to study the influence of the microstructure on the sorption kinetics. Significant changes of the volume fraction distributions are found for samples containing the catalyst chromium oxide, particularly when the catalyst particles are nanometre-sized. Cr2O3 is an effective agent for breaking up particles during the milling process. The comparison of SANS and SAXS curves give some of the first information about the distribution of hydrogen-containing structures. Using anomalous small-angle X-ray scattering, an energy-dependent scattering is found for an MgHx sample with 1 mol% Fe2O3. From the separated scattering curve a size distribution of hard spheres is obtained with a size range which is expected for crystallite and particle sizes of the Fe2O3 catalyst. Chemical shifts in the absorption spectra give information about the stability of the metal oxide catalysts during the milling process.

Structure and dynamics of thin polymer films using synchrotron X-ray scattering

Jiang, Z. — 2007-04-21

Recent measurements of the scattering function and of the dynamics of surface and interfacial fluctuations in thin supported molten films and bilayers using synchrotron X-ray diffuse scattering and photon correlation spectroscopy in reflection geometry are reported. The results for monolayer films thicker than four times of the radius of gyration of polystyrene show behavior of normal over-damped capillary waves expected for the surface fluctuations of a viscous liquid. However, thinner films show deviations indicating the need to account for viscoelasticity. The theory has been extended to the surface and interfacial modes in a bilayer film system. The results are discussed in terms of surface tension, viscosity and shear modulus. Also recent experiments to measure the isothermal compressibility of supported polystyrene films by studying `bulk' scattering from the interior of the films is discussed.

Structural changes in gradient colloidal thin gold films deposited from aqueous solution

Roth, S.V. — 2007-04-21

Pattern formation is investigated in a one-dimensional gradient prepared from an aqueous colloidal gold nanoparticle solution. The hydrodynamic process can be reconstructed by determining the prominent length scales and surface roughness in the dried gradient. The structural information is obtained using a combination of grazing-incidence small-angle X-ray scattering, which is a method of high-statistical relevance, and a moderate microfocused beam. This allows for scanning the gradient and to locally reveal the structure of the thin film. Our results, based on a simplified hydrodynamic model, indicate a system oscillating between depleted regions, nanoparticle domains and complete nanoparticle layers.

Scanning X-ray imaging with small-angle scattering contrast

Gourrier, A. — 2007-04-21

An X-ray scanning imaging technique using the integrated intensity of the small-angle X-ray scattering (SAXS) signal is presented. The technique is based on two-dimensional scanning of a thin sample section with an X-ray microbeam, collecting SAXS patterns at every scanning step using a two-dimensional detector. The integrated intensity within pre-defined regions of interest of the SAXS patterns is used to image bulk nanostructural features in the specimen with micrometre resolution which are usually not accessible by other methods such as light microscopy or scanning electron microscopy. The possibilities and limitations of the method are discussed with particular emphasis on the sources of contrast in the SAXS region for three biological specimens: cortical bone, eggshell and hair. Two main sources of image contrast are identified in the form of orientation effects for strongly anisotropic systems like cortical bone and differences in the local volume fraction of the scattering entities in eggshell. Moreover, other parameters than the integrated intensity can be quantitatively deduced from the SAXS patterns, for instance, the mean thickness of mineral platelets in bone or the strain distributions in a hair deformed plastically by microindentation.

Shape of α-crystallin analyzed by small-angle neutron scattering

Sugiyama, M. — 2007-04-21

The size and shape of aggregates of human recombinant αA-crystallin and αB-crystallin are investigated with small-angle neutron scattering and dynamic light scattering. At a bioactive temperature (310 K), both polypeptides form aggregates with almost the same size and shape. The αB-crystallin maintains an almost identical size and shape at 310 and 288 K, whereas the aggregate of αA-crystallin shows deformation at 288 K. This result suggests that at the lower temperature there is a difference in structural stability between the two aggregates of the polypeptides.

The two-Yukawa model and its applications: the cases of charged proteins and copolymer micellar solutions

Chen, S.-H. — 2007-04-21

Charged and uncharged colloidal systems are known from experiment to display an extremely rich phase behavior, which is ultimately determined by the effective pair potential between particles in solution. As a confirmation, the recent striking observation of an equilibrium cluster phase in charged globular protein solutions [Stradner, Sedgwick, Cardinaux, Poon, Egelhaaf & Schurtenberger (2004). Nature, 432, 492–495] has been interpreted as the effect of competing short-range attractive and long-range repulsive interactions. The `two-Yukawa (2Y) fluid' model assumes an interparticle potential consisting of a hard core plus an attractive and a repulsive Yukawa tail. We show that this rather simple model can indeed explain satisfactorily the structural properties of diverse colloidal materials, measured in small-angle neutron scattering (SANS) experiments, including the cases of equilibrium cluster formation and soft-core repulsion. We apply this model to the analysis of SANS data from horse-heart cytochrome c protein solutions (whose effective potential can be modeled as a hard-sphere part plus a short-range attraction and a weaker screened electrostatic repulsion) and micellar solutions of a triblock copolymer (whose effective potential can be modeled as a hard-sphere part plus a repulsive shoulder and a short-range attraction). The accuracy of the 2Y model predictions is successfully tested against Monte Carlo simulations in both cases.

Performance of the 36 m small-angle neutron scattering spectrometer at BATAN, Serpong, Indonesia

Putra, E.G.R. — 2007-04-21

A 36 m small-angle neutron scattering (SANS) spectrometer (SMARTer) has been installed at the end of a 49 m long neutron guide tube and located in the neutron guide hall at the Neutron Scattering Laboratory (NSL), Serpong, Indonesia. At present, this is the largest SANS spectrometer in the Asia–Pacific region and consists of an 18 m long tube collimation system and another 18 m long tube to accommodate a 128 × 128 3He two-dimensional position-sensitive detector. The detector can be moved continuously from 1.5 to 18 m and can be shifted laterally by 0.1 m to cover a large range of Q, where Q is the magnitude of the scattering vector given by Q = (4\pi /\lambda) \sin (\theta /2), θ is the scattering angle and λ is the wavelength. By selecting the rotational speed of the velocity selector, the incident thermal neutron beam will have a wavelength λ in the range 3–6 Å and a Q range of 0.002–0.6 Å−1. The maximum neutron flux at the sample position is 4 × 106 neutrons cm−2 s−1. Measurements of some standard samples using SMARTer are reported for inter-laboratory comparisons that show, for the first time, how SMARTer's capabilities compare with those of other prominent SANS instruments.

Wide-q observation from 10−4 to 2.0 Å−1 using a focusing and polarized neutron small-angle scattering spectrometer, SANS-J-II

Iwase, H. — 2007-04-21

In order to extend an upper q-limit [q is the magnitude of the scattering vector q, defined by q = (4π/λ)sinθ, where λ and 2θ are the wavelength and the scattering angle, respectively], high-angle 3He sub-detectors were installed on a focusing and polarized neutron small-angle scattering spectrometer (SANS-J-II) at JRR-3, Tokai, Japan. Consequently, the upper q-limit was improved from 0.2 to 2.0 Å−1. To quantitatively discriminate spin incoherent scattering from hydrogen or to perform nuclear spin polarization contrast variation, a remanent supermirror analyser is also available on the high-angle sub-detector. By combining a focusing ultra-small-angle scattering, realised by compound and/or magnetic lens and high-resolution area detector, SANS-J-II is able to cover from 3 × 10−4 to 2.0 Å−1 (four orders of magnitude of q), which benefits investigation of hierarchically ordered systems, found widely in hard, soft and bio-materials.

Monte Carlo simulations of the new small-angle neutron scattering instrument SANS-1 at the Heinz Maier-Leibnitz Forschungsneutronenquelle

Gilles, R. — 2007-04-21

A new small-angle scattering instrument SANS-1 will be installed on beamline NL 4a at the Heinz Maier-Leibnitz Forschungsneutronenquelle (FRM II). It is a joint venture between the Technische Universität München and the Geesthacht Neutron Facility (GENF). SANS-1 has been optimized to be one of the most intense and versatile small-angle scattering instruments within the boundaries of available space and interaction with neighbouring instruments. Using the program McStas, the dimensions and the features of the different optical components were investigated and compared for the final selection. A vertical S-shaped neutron guide, a tower with two possible selectors, one for medium resolution at high intensity and one for high resolution, and two optimized transmission polarizers are the main advantages of SANS-1 compared with traditional instruments at other facilities.

Small-angle X-ray scattering study on conformation of poly(sodium l-glutamate) in NaCl and NaF aqueous solutions

Shimizu, S. — 2007-04-21

The effect of anions F− and Cl− on the conformation of poly(sodium l-glutamate) (PNaGA) in added-salt aqueous solution was studied using potentiometric titration, high-resolution proton nuclear magnetic resonance (NMR), circular dichroism (CD) and small-angle X-ray scattering (SAXS) techniques. In the titration curve for PNaGA in NaCl aqueous solution, four conformation regions, i.e. aggregation-, helical-, helix-to-coil transition- and random-coiled, were clearly observed but these regions were gradually obscured when the concentration of F− was increased. Both CD and NMR spectra have clarified that the local conformation of PNaGA in NaF aqueous solution is a random-coiled state, independent of the degree of neutralization (DN). SAXS studies show that the conformation of a larger dimension for PNaGA having DN = 0.25 in 0.2 NaF aqueous solution is roughly mimicked by a worm-like chain having persistence length of ca 5.9 Å, but the conformation at DN = 0.80 is far from an isolated worm-like chain.

Microstructure of ternary system di-lauroyl-phosphatidyl-adenosine/water/cyclohexane

Betti, F. — 2007-04-21

1,2-Dilauroyl-sn-glycero-3-phosphatidyl-adenosine in 0.1 M phosphate buffer (pH = 7.5) forms worm-like micelles that with ageing of the solution, self-assemble into helical superstructures. Small-angle neutron scattering has shown that dissolution of even small amounts of oil in the hydrophobic cores induces a dramatic structural transition to form spherical micelles. A variation of the interfacial film curvature promotes a strong change in base–base interaction pattern as shown in circular dichroism experiments.

Modelling of bacteriophage capsids and free nucleic acids

Zipper, P. — 2007-04-21

The reconstruction of sphere shells as realized in bacteriophage capsids can be achieved by ab initio modelling approaches based on a genetic algorithm or simulated annealing. The application of tight constraints such as icosahedral symmetry makes the DAMMIN procedure the method of choice. The ab initio models obtained may be compared with three-dimensional models derived from crystal data. This information, in conjunction with surface calculations and application of specific hydration algorithms, allows the generation of biophysically relevant hydrated three-dimensional models. Modelling free RNA of viruses represents another challenge to advanced modelling intentions. While application of the DAMMIN procedure provides the generation of appropriate models for the overall structure of nucleic acids, inclusion of further constraints improves the biological relevance of the resultant models. This may be achieved by our in-house program SUBSTRUCT, which allows involvement of secondary structure details.

Biological solution scattering: recent achievements and future challenges

Grossmann, J.G. — 2007-04-21

In the post-genomic age it is apparent that as structures of larger macromolecules and their complexes are investigated, structure–function investigations are often confronted with the necessity to apply a portfolio of tools for biochemical and biophysical characterization. A survey of the published literature over the last decade reveals that publications in the area of structural biology employing neutron or X-ray scattering as one of their techniques tripled since 1995. Yet, taken as a whole, the contribution from small-angle scattering (SAS) to research papers dealing with structural analyses is still only of the order of 1% in 2005 (for comparison, less than 0.5% in 1995). Nevertheless, the last few years saw stimulating biological applications and analysis procedures which emphasize the growing potential of SAS applications for the structural studies of macromolecules in solution. The usage of SAS largely consists of low-resolution reconstructions of molecules with partial or without presumption of structural details, consistency analysis of high-resolution crystallographic structures and their corresponding low-resolution models determined in the solution state, and rigid-body refinement of multi-subunit assemblies including complexes and full-length multidomain proteins. Complementary structural information obtained from SAS in conjunction with data acquired by protein crystallography, NMR, molecular dynamics or computational docking provides a means to link low- and high-resolution models essential for the elucidation of biomolecular organization, interactions and function. The capabilities as well as limitations of determining low-resolution structures of multidomain proteins, macromolecular complexes and assemblies are highlighted in three examples. The first example is the characterization of the conformation of the PDZ region of SAP97, a multidomain protein involved in the regulation and localization of membrane receptor molecules. The second example is the characterization of the structural features of the TIM10 complex, an escort molecule for mitochondrial inner-membrane proteins, and the third example is the description of the shape and pH-induced conformational transition of a full-length bacterial potassium channel. The latter two in particular benefited from neutron scattering with contrast variation by using H–D labelling of the macromolecular complex or the solvent, respectively.

Analysis of small-angle X-ray scattering data of protein–detergent complexes by singular value decomposition

Lipfert, J. — 2007-04-21

Small-angle X-ray scattering can be a valuable tool in the structural characterization of membrane protein–detergent complexes (PDCs). However, a major challenge is to separate the PDC scattering signal from that of the `empty' detergent micelle in a protein–detergent mixture. We briefly review an approach that allows approximate determination of the PDC scattering signal at low momentum transfer and present a novel approach that employs a singular value decomposition (SVD) and fitting of scattering data collected at different protein–detergent stoichiometries. The SVD approach allows the scattering profile for the PDC over the entire measured momentum transfer range to be obtained, it is applicable to strongly scattering detergents and can take into account interparticle interference. The two approaches are contrasted and an application to the membrane protein TM0026 from Thermotoga maritima is presented.

In situ investigation of annealing effect on lamellar stacking structure of polyethylene thin films by synchrotron grazing-incidence small-angle and wide-angle X-ray scattering

Sasaki, S. — 2007-04-21

We have investigated lamellar stacking structure of melt-crystallized and annealed high-density polyethylene (HDPE) thin films, with a thickness of ca 400 nm prepared on silicon wafers, using synchrotron grazing-incidence small-angle and wide-angle X-ray scattering (GISWAXS) measurements at the BL40B2 beamline in SPring-8. In-situ measurements of GISWAXS were carried out for the films in a stepwise annealing process under vacuum. Scattering peaks relating to the long period, the average distance between stacked crystalline lamellae, were measured only in the in-plane direction near the Yoneda peak of the grazing-incidence small-angle X-ray scattering patterns. On the other hand, the orthorhombic (110) and (200) reflections of oriented HDPE crystals were measured in the out-of-plane direction of the grazing-incidence wide-angle X-ray scattering patterns. It was revealed that crystalline lamellae were stacked in a parallel direction to the film surface and the long period increased from ca 25 nm to ca 32 nm in a stepwise annealing process. Within a lamella, molecular chains were found to be packed regularly and the chain axis (the c axis) was relatively oriented parallel to the film surface.

Contribution of small-angle X-ray scattering to microstructural investigation of newly developed Mg–rare earth alloys for structural applications

Antion, C. — 2007-04-21

New Mg–Y–Gd–Mn alloys, strengthened by a dense fine scale precipitation, have been recently designed for structural applications up to 523 K. The qualitative small-angle X-ray scattering study presented here enlightens the mechanical properties at high temperature of these alloys. Small Guinier–Preston zones have been evidenced in alloys maintained at room temperature after quenching. The metastable phases, studied in parallel using high-resolution transmission electron microscopy and responsible for the good mechanical properties, are difficult to quantify completely owing to their complex microstructure of interconnected globular and faceted precipitates.

Small-angle fibre diffraction studies of corneal matrix structure: a depth-profiled investigation of the human eye-bank cornea

Quantock, A.J. — 2007-04-21

In the cornea of the eye light transmission is facilitated by the regular arrangement and uniform diameter of collagen fibrils that constitute the bulk of the extracellular corneal matrix. Matrix architecture, in turn, is believed to be governed by interactions between collagen fibrils and proteoglycan molecules modified with sulfated glycosaminoglycan side chains. Here, we outline the contribution made by small-angle X-ray scattering studies of the cornea in understanding the role of sulfated glycosaminoglycans in the control of collagen architecture in cornea, and present new depth-profiled microbeam data from swollen human eye-bank corneas that indicate no significant change in collagen fibril diameter throughout the tissue, but a lower collagen interfibrillar spacing in the anterior-most stromal regions compared with the ultrastructure of the deeper cornea.

Anomalous grazing-incidence small-angle X-ray scattering investigation on the surface morphology of an FePt magnetic nanoparticle monolayer on functional modulated substrates

Huang, T.-W. — 2007-04-21

The structural stability and coalescence of self-assembled FePt monolayer nanoparticles on functional substrates with/without an Au overlayer during annealing were studied. From X-ray diffraction and the anomalous grazing-incidence small-angle X-ray scattering techniques, the nanoparticles were found to be intact under the annealing process when a 5–10 nm overlayer of Au was deposited on top of FePt monolayer nanoparticles. From the simulation result, the particle size 4.5 ± 0.5 nm is typically unchanged, but the distance between particles is reduced from 7.5 ± 1.5 nm to 5.5 ± 1.1 nm after annealing. The results suggest that the 5 nm Au coverlayer is an effective diffusing barrier layer to prevent the FePt nanoparticles from sintering during the annealing process.

Polarized small-angle neutron scattering study of two-dimensional spatially ordered systems of nickel nanowires

Grigoryeva, N.A. — 2007-04-21

The magnetic and structural properties of two-dimensional spatially ordered systems of ferromagnetic nickel nanowires embedded into an Al2O3 matrix have been studied using polarized small-angle neutron scattering (polarized SANS). We measured the total (nuclear and magnetic) scattering I(q) as a polarization-independent scattering, the field-dependent scattering as IH(q) = I(q, H) − I(q, 0), where H is the magnetic field, and the nuclear-magnetic interference as a polarization-dependent (P) scattering ΔI(q, P). A typical scattering pattern is composed of the diffuse small-angle scattering and the Bragg peak. It is shown that the introduction of Ni into the matrix does not change the position of the Bragg peak but results in an increase of the scattering intensity both in the small-angle region and at the Bragg positions. An external magnetic field was applied perpendicular or parallel to the long dimension of the nanowires in order to reveal the anisotropic properties of the magnetic system. It is shown that, firstly, the magnetic-field-dependent scattering IH(q) provides new and principally different information as compared with the interference term ΔI(q). Secondly, two contributions to the interference term ΔI(q) (ascribed to the diffuse scattering and to the diffraction peaks) have different signs indicating different origins of the scattering objects. Thirdly, polarized SANS gives a detailed picture of the magnetization process, which could not be obtained by methods of standard magnetometry.

Spin-echo small-angle neutron scattering study of the domain structure of an Ni layer on a Cu substrate

Grigoriev, S.V. — 2007-04-21

Spin-echo small-angle neutron scattering (SESANS) is used to study the magnetic domain structure of an Ni layer electrodeposited onto a Cu substrate. The domain structure of the sample corresponds to the hard-plane model, where the magnetization in the domains is directed perpendicular to the layer; the domain length coincides with the thickness of the layer of the order of 10 µm and its width is of the order of 1 µm. The pair correlation function of the magnetization has been directly measured. It is established that the width of the domain depends linearly on its thickness. The domain structure does not depend on heating at temperatures below T_{\rm C} of nickel. Annealing at T\, \gt\, T_{\rm C} results in a reconstruction of the domain structure with a tendency to the easy-plane model, i.e. with domain magnetization in the plane. The multiple scattering effect is studied and may be taken into account. This experiment demonstrates the possibilities of magnetic SESANS. Some aspects of this novel technique are pointed out.

Microstructural investigation of low-dose neutron irradiation effects in martensitic steels for nuclear application by means of small-angle neutron scattering

Coppola, R. — 2007-04-21

The microstructural effect of low-dose neutron irradiation and subsequent high-temperature tempering in the reduced activation ferritic/martensitic steel F82H-mod. (7.73 Cr, 0.09 C, 0.08 Mn, 0.19 V, 2.06 W, 0.02 Ta, wt%, bal. Fe) has been studied using small-angle neutron scattering (SANS). The investigated samples were irradiated with thermal neutrons at 523 K, to dose levels of 2.4 displacements per atom then tempered for 2 h at 1043 K. The SANS measurements were carried out at the D22 instrument of the High Flux Reactor at the Institut Max von Laue–Paul Langevin, Grenoble, France. The differences observed in nuclear and magnetic small-angle neutron scattering cross-sections after subtraction of the reference sample from the irradiated one suggest that the irradiation and the subsequent post-irradiation tempering produce the growth of non-magnetic precipitates; the results are also compared with those obtained on other ferritic/martensitic steels, with different chemical composition, irradiated under the same conditions.

Unraveling the equilibrium chain exchange kinetics of polymeric micelles using small-angle neutron scattering – architectural and topological effects

Lund, R. — 2007-04-21

In this paper, we present a study of micellar structures formed by poly(styrene)-poly(butadiene) (PS10-PB10; the numbers indicate the molecular weight in kg mol−1) diblock copolymers and PB10-PS20-PB10 triblock copolymers in different n-alkane solvents. Particular emphasis is placed on the dynamic properties of these micelles under equilibrium which are studied using a novel time-resolved small-angle neutron scattering technique. The results show that the structures of the micelles are very similar for both the diblock and triblock copolymers, which allows a direct comparison of the dynamic properties. A novel logarithmic relaxation is found for both the triblock and the diblock micelles which is not consistent with theoretical expectations. However, for the diblock micelles, the relaxation kinetics seem to approach the rate and the single exponential decay predicted by Halperin & Alexander [Macromolecules, (1989), 22, 2403–2412] when the micellar cores are strongly swollen with solvent. For the triblock micelles a logarithmic relaxation is found for all cases as an effect of additional topological knots present even in highly swollen micellar cores. This behavior is assigned to an increased coupling of chain motion within the dense confined core – an effect which seems to vanish in diblock micelles when the core is sufficiently swollen.

Residual orientation in micro-injection molded parts

Healy, J. — 2007-04-21

The residual orientation following micro-injection molding of small rectangular plates with linear polyethylene has been examined using small-angle neutron scattering, and small- and wide-angle X-ray scattering. The effect of changing the molding conditions has been examined, and the residual chain orientation has been compared to the residual orientation of the crystallites as a function of position in the sample. This study has found that, for micromoldings, the orientation of the crystallites decreases with increasing injection speed and increasing mold thickness. The combined data suggest that the majority of the orientation present comes from oriented crystal growth rather than residual chain orientation.

On the heterogeneous character of water's amorphous polymorphism

Koza, M.M. — 2007-04-21

In this paper we report in situ small-angle neutron scattering results on the high-density amorphous (HDA) and low-density amorphous (LDA) ice structures and on intermediate structures as found during the temperature-induced transformation of HDA into LDA. We show that the small-angle signal is characterized by two Q regimes featuring different properties [Q is the modulus of the scattering vector defined as Q = (4\pi/\lambda_{\rm i})\sin(\theta) with \theta being half the scattering angle and \lambda_{\rm i} the incident neutron wavelength]. The very low Q regime (\lt\, \sim \!5\times 10^{-2} Å−1) is dominated by a Porod-limit scattering. Its intensity reduces during the course of the HDA-to-LDA transformation following kinetics reminiscent of those observed in wide-angle diffraction experiments. The small-angle neutron scattering form factor in the intermediate regime of 5 \times 10^{-2} \,\lt\, Q \,\lt\, 0.5 Å−1 for HDA and LDA features a rather flat plateau. However, the HDA signal shows an ascending intensity towards smaller Q marking this amorphous structure as heterogeneous. When following the HDA-to-LDA transition, the form factor shows a pronounced transient excess in intensity marking all intermediate structures as strongly heterogeneous on a length scale of some nanometres.

Structural study of nanocrystalline nickel thin films

Radic, N. — 2007-04-21

Nickel thin films (400 nm) were deposited by magnetron sputtering onto fused silica substrates. The effects of argon pressure and substrate temperature (from room temperature to 973 K) upon the film structure were investigated. The film structure was studied using grazing-incidence small-angle X-ray scattering (GISAXS) and X-ray diffraction (XRD) analysis. It was found that the prepared nanocrystalline Ni films contain two kinds of inhomogeneities observable by GISAXS, namely isotropic and platelet-like. Up to about 373 K the isotropic or spherical `particles' prevail, while above that temperature the platelet-like `particles' predominate. These inhomogeneities are ascribed to intergranular matter or grain boundaries, since the grain size (as determined from the XRD patterns) was found to increase from 7 nm in samples deposited at room temperature to about 90 nm in samples deposited at 423 K or higher temperature.

Melting behavior of polymorphic crystals of poly(trimethylene 2,6-naphthalate) studied by simultaneous synchrotron X-ray scattering and thermal analysis

Chuang, W.-T. — 2007-04-21

The polymorphic crystallization and melting behavior of poly(trimethylene 2,6-naphthalate) (PTN) have been investigated using small-angle X-ray scattering and simultaneous wide-angle X-ray scattering (WAXS) and differential scanning calorimetry (DSC). The α-crystal, the β-crystal and the coexistence of both crystal forms of PTN develop at an isothermal temperature below 393 K, above 453 K and between these two temperatures, respectively. The simultaneous WAXS/DSC measurement provides a good way to identify the origin of multiple melting peaks and to get equilibrium melting temperatures. During the PTN melting process, the thermal evolutions of crystallinities, Bragg diffraction intensities and DSC thermograms reveal that the \alpha \rightarrow \beta phase transformation and primary and secondary crystallizations arise to generate the multiple melting peaks. The β-crystal with high equilibrium melting temperature (T^{0}_{{\rm m},\beta}} = 510 K) is a structurally stable phase while the α-crystal with low equilibrium melting temperature (T^{0}_{{\rm m},\alpha}} = 488 K) is a metastable phase. The temperature-dependent structural parameters such as the long period, lamellar thickness and amorphous thickness were extracted from the interface distribution function. Two-step changes in the lamellar thickness and the invariant during the subsequent melting of PTN crystallized at 383 K are consistent with the \alpha \rightarrow \beta transformation obtained by WAXS/DSC. The \alpha \rightarrow \beta transformation, a typical melting–recrystallization, proceeds firstly via surface melting of α-lamellae, and then the PTN chains near the boundaries of surviving α-lamellae modify their conformation to form the β-crystal resulting in thickening lamellae.

Fractal aggregates of the Pt nanoparticles synthesized by the polyol process and poly(N-vinyl-2-pyrrolidone) reduction

Lin, J.-M. — 2007-04-21

Small-angle X-ray scattering was used to characterize the size and aggregation behavior of the Pt nanoparticles synthesized by the polyol process and the unusual poly(N-vinyl-2-pyrrolidone) (PVP) reduction. With formaldehyde (HCHO) as the reduction agent, the Pt nanoparticles synthesized in aqueous solutions with a high PVP/PtCl4 weight ratio were characterized by short rods with a 70% polydispersity in rod length. The size and size distribution of the rod-like Pt nanoparticles (3 nm in rod length and 2 nm in rod diameter) are consistent with the corresponding transmission electron microscopy image. With a comparable PVP/PtCl4 weight ratio in the aqueous solution containing HCHO, the high number density of reduced Pt nanoparticles led to a fractal-like aggregation with a fractal dimension of 2.1 and a correlation length of ~30 nm. We also demonstrated that Pt nanoparticles can be synthesized by PVP reduction at 323 K without HCHO. The particle size and the clustering behavior of the Pt nanoparticles reduced by PVP are closely related to the PVP concentration in the solution. Both the Pt nanoparticles synthesized in the commonly used polyol process and the unusual PVP reduction form fractal-like clusters via the PVP–metal nanoparticle association when the number density of the Pt nanoparticles in the solutions is high.

Simplified tube form factor for analysis of small-angle scattering data from carbon nanotube filled systems

Justice, R.S. — 2007-04-21

This work presents an analysis method for small-angle scattering data utilizing a simplified tube (hollow cylinder) form factor. The simplified form factor captures the rod-like character of a tube at long length scales (one-dimensional), the sheet-like character of the tube wall at intermediate length scales (two-dimensional), and the surface characteristics of a tube at small length scales while suppressing the deep minima seen in the exact form factor. Ultra-small-angle X-ray scattering data from composites made with multi-walled carbon nanotubes and a bismaleimide resin are analyzed using the simplified form factor and compared with scanning electron micrographs. Although a hollow core is not evident via microscopy, a solid rod form factor does not fit the data. However, a tube form factor does fit the data and generates reasonable geometric parameters. At higher concentrations, evidence for aggregation is seen in the data. Aggregation is accommodated by including a fractal structure factor within the simplified approach, allowing facile analysis of data from aggregated (poorly dispersed) fillers.

In situ and time-resolved ultra small-angle neutron scattering observation on growing poly(methyl methacrylate)-block-polystyrene via reversible addition–fragmentation chain transfer living radical polymerization

Motokawa, R. — 2007-04-21

Reversible addition–fragmentation chain transfer (RAFT) living radical polymerization of poly(methyl methacrylate)-block-polystyrene (PMMA-b-PS) was investigated by a combined method of gel permeation chromatography (GPC) and in situ and time-resolved ultra small-angle neutron scattering (tr-USANS) measurements. GPC enables us to examine a growing single molecule as a function of polymerization time, with respect to monomer conversion, molecular weight (Mn) and polydispersity index (Mw/Mn) of PMMA-b-PS. On the other hand, tr-USANS, observing in meso-length scales from nm to µm, reveals polymerization-induced molecular self-assembly, such as microphase separation by PMMA-b-PS or macrophase separation between PMMA-b-PS and homo-polystyrene (by-product). By combining these two experimental methods, we elucidated that RAFT living polymerization was retarded by micro- and macrophase separations.

From CIF to virtual morphology using the WinXMorph program

Kaminsky, W. — 2007-04-01

Crystal morphologies are predicted from data stored in files in the CIF format (crystallographic information file standard of the International Union of Crystallography) on the basis of the Bravais–Friedel, Donnay–Harker model. Several simple improvements to the calculation are introduced with WinXMorph, version 1.4.9, in conjunction with illustrations of the morphologies of quartz, sucrose, lactose, pyrite and lysozyme. The morphologies of the recently discovered pentamorphs of 1,8-dihydroxyanthraquinone are predicted. WinXMorph is available free-of-charge for educational use.

A focusing-geometry small-angle neutron scattering instrument with a magnetic neutron lens

Oku, T. — 2007-04-21

We have constructed a focusing-geometry small-angle neutron scattering (FSANS) instrument, SANS-J-II, with two kinds of neutron focusing device: a series of compound refractive lenses made of MgF2 and a magnetic neutron lens based on an extended Halbach-type sextupole magnet. In this study, we investigated the performance of the FSANS instrument with the magnetic neutron lens. The intensity distribution of a direct neutron beam focused on the detector plane by the magnetic neutron lens had a ratio of the peak height to the background level of \sim\!6\times 10^4 for a polarized neutron beam with a polarization degree of \sim \!0.99. It is found that a minimum value of the measurable q range [where q is the modulus of the scattering vector and is defined as q = (4\pi/\lambda)\sin(\theta/2), where \theta is the scattering angle and \lambda is the neutron wavelength], q_{\rm min}, of 6.5 \times 10^{-4} Å−1 can be achieved by the FSANS instrument with the magnetic neutron lens using neutrons with \lambda = 6.6 Å and \Delta \lambda/\lambda = 0.13 for the full width at half maximum.

Contrast variation in X-ray and neutron scattering

Stuhrmann, H.B. — 2007-04-21

This contribution is meant to highlight some progress in those areas of contrast variation which are known to be technically more difficult but which promise interesting applications. These concern the use of the anomalous dispersion of light elements, like sulfur and phosphorus in structural studies and experiments of polarized neutron scattering from nuclear spin polarized samples.

Homodyne and heterodyne X-ray photon correlation spectroscopy: latex particles and elastomers

Livet, F. — 2007-04-21

In a coherent X-ray small-angle experiment, heterodyning between the scattering amplitudes of two samples is obtained by stacking a static reference and a fluctuating sample. Results of homodyne and heterodyne measurements are compared in the case of 98 nm diameter latex particles in glycerol. The method is also used for the study of the slow relaxation process of carbon-black-filled ethylene–propylene elastomers corresponding to the relaxation of the carbon black skeleton after a 100% elongation. On the scale of the 10 µm coherent beam, heterodyning is used to separate fluctuations from long-term flowing of the sample. We show that this flow can be observed for about 10 h, with velocities of the order of nanometres per second. Random fluctuations are dominant in the speckle changes only for large q values (q > 2 × 10−2 Å−1) and after a long relaxation time.

Precursory microstructures in Zr–Cu–Al–Ni bulk metallic glasses examined by anomalous small-angle scattering at the Zr K edge

Okuda, H. — 2007-04-21

Anomalous small-angle X-ray scattering measurements of Zr–Cu–Al–Ni quaternary alloys have been made at the Zr K absorption edge. In melt-quenched samples, small cluster components without crystallization were found. The contrast change at the edge suggested that compositional fluctuation of Al is incorporated.

A modified Ising model for the thermodynamic properties of local and global protein folding–unfolding observed by circular dichroism and small-angle X-ray scattering

Shiu, Y.-J. — 2007-04-21

Based on the mean-field approximation, we have applied a modified Ising model to describe general protein unfolding behavior at thermodynamic equilibrium with the free energy contributed by the subgroup units (amino acids or peptide bonds) of the protein. With the thermodynamic properties of the protein, this model can associate the stepwise change of an unfolding fraction ratio profile with the local and global conformation unfolding. Taking cytochrome c (cyt c) as a model protein, we have observed, using small-angle X-ray scattering and circular dichroism (CD), the global and local structure changes for the protein in three kinds of denaturant environments: acid, urea and guanidine hydrochloride. The small-angle X-ray scattering and CD results are mapped to the unfolding fractions as a function of the pH value or denaturant concentration, from which we have extracted local and global unfolding free energies of cyt c in different denaturant environments using a modified Ising model. Based on the characteristics of the thermodynamic properties deduced from the local and global protein folding–unfolding, we discuss the thermodynamic stabilities of the protein in the three denaturant environments, and the possible correlation between the global conformation change of the protein and the local unfolding activities of the S—Fe bond in the Met80-heme and the α-helices.

A combined small-angle scattering study of a chemical reaction at specific sites and reaction-induced self-assembly as a problem in open non-equilibrium phenomena

Hashimoto, T. — 2007-04-21

As a problem in open non-equilibrium phenomena, small-angle scattering (SAS) studies of chemical reactions at specific sites and reaction-induced self-assembly of a system which is obtained by mixing two stable solutions of palladium acetate [Pd(OAc)2] in N,N-dimethylformamide and the second-generation polyamidoamine dendrimer in methanol are presented. The self-assembly was studied using a combination of neutron and X-ray SAS. The results revealed that the self-assembly involves the initial formation of aggregates of an average radius of 20 nm composed of the dendrimers and Pd(OAc)2 followed by formation of palladium nanoparticles of a radius of 2.0 nm inside the aggregates. The aggregates were found to provide a special field for a chemical reaction for reduction of Pd(II) ions with methanol and for the self-assembly of the reduction products of Pd(0) atoms into nanoparticles. The nanoparticles are found to be trapped and stabilized in the aggregates.

Collapse of the hydration shell of a protein prior to thermal unfolding

Koizumi, M. — 2007-04-21

Based on high statistical quality wide-angle X-ray scattering data for the unfolding–refolding process of hen egg-white lysozyme (HEWL), we have analysed the change of the hydration shell as a function temperature using the program CRYSOL. The present results suggest that the decrease of the hydration-shell density starts from a lower temperature than the transition temperature of the collapse of the tertiary structure of HEWL. Although the use of CRYSOL for scattering data for proteins before the transition has an apparent limitation, the collapse of the hydration shell prior to the unfolding of HEWL agrees with a slight tendency of the radius of gyration to decrease during the thermal unfolding process.

A small-angle X-ray scattering study of the effect of chain architecture on the shear-induced crystallization of branched and linear poly(ethylene terephthalate)

Hanley, T. — 2007-04-21

The synchrotron-based small-angle X-ray scattering (SAXS) technique was used to investigate the shear-induced crystallization kinetics of branched/unbranched poly(ethylene terephthalate) (PET). Reactive extrusion of bottle-grade PET with the branching and chain-extension agents pyromellitic dianhydride and pentaerythritol results in enhanced rheological properties, such as higher melt strength and higher viscosity. In this study, six samples of PET were investigated: linear PET [intrinsic viscosity (IV) ≃ 0.76 dm3 g−1]; four branched PETs produced from linear PET by a reactive extrusion technique (IV ≃ 0.86–1.06 dm3 g−1); and a control PET (IV ≃ 0.73 dm3 g−1) extruded under the same conditions without reactive agents. SAXS data were recorded for the PET at the melt temperature and time-resolved SAXS data were recorded following the application of a step shear (53 s−1 for 2 s). As the PET IV was increased, the extent of shear-induced orientation increased, whilst the time taken for the polymer to initiate and complete crystallization decreased.

Concentration fluctuations induced by orientation fluctuations in polybutadiene–4-cyano-4'-n-octylbiphenyl mixtures

Shimizu, H. — 2007-04-21

The changes in concentration fluctuations of polymer–liquid crystal (LC) binary mixtures with temperature were investigated by small-angle X-ray scattering in their one-phase region and in the isotropic state of the LC. The concentration fluctuations consist of two modes: an OZD mode expressed by the Ornstein–Zernike–Debye equation with a correlation length ξ and a DB mode expressed by the Debye–Buche equation with a correlation length l. The temperature dependence of the OZD mode exhibits critical phenomena similar to common binary mixtures. Under the condition where the LC molecules are oriented by an electric field, the OZD mode is insensitive to the orientation while the DB mode is enhanced perpendicular to the orientation direction. These results indicate that the DB mode is induced by the orientation of the LC molecules.

ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis

Petoukhov, M.V. — 2007-04-21

Small-angle scattering (SAS) is frequently employed for screening large numbers of samples and for studying these samples under different conditions, including space- and time-resolved analysis. These measurements produce immense amounts of data, especially on modern high-flux and high-brilliance sources (e.g. third-generation synchrotrons). In biological SAS, like high-throughput macromolecular crystallography, large-scale analysis of proteins and macromolecular complexes is also emerging. Automation of data analysis becomes an indispensable prerequisite for adequate evaluation of high-throughput SAS experiments. Here a prototype of an automated data-analysis system for isotropic solution scattering based on the further development of the programs belonging to the package ATSAS 2.1 is reported. This system allows the major analysis tasks starting from the raw data processing and, for monodisperse systems, finishing with a three-dimensional model, to be performed automatically. Convenient web interfaces for the online use of individual ATSAS programs are also provided.

Reverse Monte Carlo analysis for small-angle scattering of expanded fluid Hg: connection to the wide-angle structure factor

Hagita, K. — 2007-04-21

A preliminary result of reverse Monte Carlo (RMC) analysis of small-angle X-ray scattering data for expanded fluid Hg with the help of wide-angle X-ray diffraction data in the same thermodynamic state is presented. In RMC analysis, three-dimensional configurations of 100000 Hg atoms were modeled to see the large density fluctuation associated with liquid–vapor critical phenomena. It was found that interpolation of measured structure factors is necessary for RMC analysis.

Two-dimensional small-angle X-ray scattering from as-grown and heat-treated synthetic quartz

Guzzo, P.L. — 2007-04-21

The small-angle X-ray scattering (SAXS) in as-grown and heat-treated quartz crystals was investigated as a function of the azimuth angle around the primary beam. For this, samples parallel to (10\bar 10) were extracted from Z- and −X-growth sectors of a synthetic quartz bar which had the OH content evaluated by infrared spectroscopy (IRS). In addition, SAXS and IRS were independently recorded as a function of heating temperature. As a result, the two-dimensional SAXS images revealed an anisotropic pattern randomly decorated by low-intensity Kossel lines. The intensities were projected along specific directions or were axially integrated around the primary beam. It was observed that the Porod invariant (Q) increased and the Kossel lines moved slightly to higher q values with increasing temperature. The effect of the sample orientation on the Q value and the lack of a clear relationship between Q and OH content suggested that the diffuse scattering due to the periodicity of the crystal lattice played an important role in the small-angle scattering of quartz. The net scattering intensities produced by heat-treatment at 873 K were attributed to molecular water aggregates created by the diffusion of as-grown OH defects.

Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering

Mylonas, E. — 2007-04-21

One of the most important overall parameters, which can be derived from small-angle X-ray scattering (SAXS) experiments on macromolecular solutions is the molecular mass (MM) of the solute. In particular, for a monodisperse protein solution, MM of the solute is calculated from the extrapolated scattering intensity at zero angle I(0). Assessing MM by SAXS provides valuable information about the oligomeric state and absence of unspecific aggregation in solution. The value of MM can either be estimated by comparison with a protein standard with a known MM or by determining the absolute scattering intensity using, e.g., water scattering. In both cases, knowledge about the solute concentration and about the partial specific volume of the protein is required. By measuring 13 well characterized globular proteins with MMs ranging from 13.7 to 669 kDa we analyze the sources of possible systematic deviations and assess the accuracy of MM determination using SAXS. The data indicate that all these proteins have approximately the same `effective' value of the partial specific volume of about 0.7425 cm3 g−1. It is shown that both inter-protein and water calibration can be used for molecular mass determination by SAXS and in most cases the errors do not exceed 10%.

X-ray reflectivity studies on the deoxyribonucleic acid adsorption by 3-β-[N-(N',N'-dimethylaminoethane)carbamoyl]cholesterol monolayer with divalent ions

Lin, T.-L. — 2007-04-21

The effect of adding divalent ions on the deoxyribonucleic acid (DNA) adsorption by a cationic lipid monolayer at the air–water interface was investigated by X-ray reflectivity on Langmuir–Blodgett films supported on silicon wafers. The films were prepared from a DC-Chol {3-β-[N-(N′,N′-dimethylaminoethane)carbamoyl]cholesterol} monolayer with 1 µM DNA in the subphase with different amounts of calcium ions added. It is found in this study that adding divalent ions, such as calcium ions, can enhance the DNA adsorption to interfaces. The adsorbed DNA layer thickness as determined by X-ray reflectivity is found to vary linearly with the square root of the ion concentration. This indicates that charge-screening effects and ion-mediated condensation play an important role in the DNA–cationic lipid monolayer interaction.

Binding of trifluoperazine to apocalmodulin revealed by a combination of small-angle X-ray scattering and nuclear magnetic resonance

Matsushima, N. — 2007-04-21

Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) studies were performed to investigate the binding of trifluoperazine (TFP) to Ca2+-free calmodulin (apoCaM) with N- and C-terminal globular domains connected by a linker. The SAXS and NMR measurements were taken throughout the titration of TFP. The SAXS analyses indicate that the binding of TFP induces structural changes from a dumbbell shape to a compact globular shape in solution. The formation of the complete globular structure requires 5.0 added equivalents of TFP. An analysis of NMR chemical-shift changes indicates that the C-terminal domain of apoCaM is involved in the binding of TFP. The SAXS and NMR data reflect the high structural flexibility of apoCaM.

Small-angle neutron scattering from extended defects in diamonds

Shiryaev, A.A. — 2007-04-21

The results of a small-angle neutron scattering investigation of natural and synthetic diamonds with variable concentrations and types of point defects and different degrees of deformation are reported. It is shown that deformation and/or annealing of diamonds lead to the formation of planar and three-dimensional defects, giving rise to small-angle scattering.

Charge interaction and temperature effects on the solution structure of lysozyme as revealed by small-angle X-ray scattering

Huang, Y.-S. — 2007-04-21

We have studied the structure of lysozyme as influenced by solution environment using small-angle X-ray scattering (SAXS). With an ellipsoid form factor and a structure factor derived using the mean spherical approximation to account for the electrostatic repulsion of lysozyme, we have extracted detailed structural information about the protein in aqueous solutions, including the size, shape, and net charge number. The SAXS data analysis shows that lysozyme in pure water, expressing an averaged net charge number of ~6, folds to an ellipsoid-like shape with a radius of gyration Rg = 16.6 Å. Temperature-dependent SAXS for lysozyme in a buffer solution in which charge repulsion has been eliminated suggests that the protein may thermally unfold gradually along a preferred direction from the ellipsoidal shape with an aspect ratio of p ≃ 2 at 303 K to an elongated shape with p ≃ 3 at 343 K. The structural parameters of the unfolded lysozyme obtained using model fitting are compared with the envelope morphology simulated using a dummy-residues model. From the evolution of the volume of lysozyme during the thermal unfolding process, we deduce a free-energy profile for the protein thermally unfolded in water using a modified Ising model on the basis of a mean field approximation.

Localization of dihalogenated phenols in vesicle systems determined by contrast variation X-ray scattering

Varga, Z. — 2007-04-21

Localization of 2,4-dichloro- and 2,4-dibromophenol in multilamellar vesicles in a 1/1 dihalogenated phenol/lipid molar ratio was investigated by classical contrast variation X-ray scattering using the isomorphous replacement method. The results were compared with those obtained by anomalous small-angle X-ray scattering from a vesicle system doped with 2,4-dibromophenol. Dissimilarities in the results of the two methods are discussed, taking into account the advantages and disadvantages of both techniques in studying multilamellar systems.

Study of amorphous nanocrystalline thin silicon films by grazing-incidence small-angle X-ray scattering

Gracin, D. — 2007-04-21

Thin Si films, with thicknesses between 100 and 400 nm, were deposited by radio frequency plasma enhanced chemical vapour deposition in silane gas (SiH4) highly diluted by hydrogen. The growing conditions were varied to obtain different degrees of crystal fractions and a variety in individual crystal sizes. The crystalline to amorphous volume fraction, as estimated by Raman spectroscopy, varied from 5 to 45% while the individual crystal sizes varied from 2 to 8 nm. The average density of the samples was estimated by using near infrared spectroscopy and the effective medium approximation. All samples were porous and contained void volume fraction between 15 and 25%. Grazing-incidence small-angle X-ray scattering has been performed at the ELETTRA synchrotron radiation source (Trieste, Italy). The scattering patterns of all examined samples indicate the presence of `particles' in the `bulk' of the thin films with gyration radii in the range of 2 to 5 nm. The higher values were found for the samples with a higher crystalline fraction. The size and the size distribution of `particles' depend upon the deposition conditions. The samples which had been deposited with a higher discharge power and a lower silane fraction had larger particles and the roughness of their surface was higher.

Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling

Lipfert, J. — 2007-04-21

Several algorithms are available to reconstruct low-resolution electron density maps of biological macromolecules from small-angle solution scattering data. These algorithms have been extensively applied to proteins and protein complexes. Here, we demonstrate their applicability to nucleic acids by reconstructing a set of RNA and DNA molecules of known three-dimensional structure from their small-angle X-ray scattering profiles. The overall size and shape of the molecules get reproduced well in all tested cases. Furthermore, we show that the generated bead models can be used as inputs for electrostatic calculations. The number of ions bound under different solution conditions computed from numerical solutions of the Poisson–Boltzmann equation for bead models agrees very well with results of calculations on all atom models derived from crystallography. The predictions from Poisson–Boltzmann theory also agree generally well with experimentally determined ion binding numbers.

A visualized analysis of small-angle neutron scattering intensity: concentration fluctuation in alcohol–water mixtures

Misawa, M. — 2007-04-21

Small-angle neutron scattering measurements have been performed on tert-butyl alcohol–water mixtures with alcohol concentrations from 0.05 to 0.30 mole fractions at 298, 313 and 328 K. Concentration fluctuations of the mixtures are analysed in terms of fractals. The structure of the concentration fluctuation is visualized by means of a large-scale reverse Monte Carlo technique. Percolation analysis of the visualized structure shows that the concentration fluctuation is characterized by polydisperse mass fractals, as found for 1-propanol–water mixtures. It seems that polydisperse mass fractals are a common structural characteristic in various alcohol–water mixtures.

Mixed magnetic phase in 6H-type BaFeO3−δ

Mori, K. — 2007-04-21

The magnetic state in 6H-type BaFeO3−δ at low temperature was studied using small-angle neutron scattering, positive-muon spin relaxation and magnetization measurements. These experiments demonstrate the appearance of two different types of magnetic states: an antiferromagnetic ordering with a long-range correlation and magnetic domains with a short-range correlation. The antiferromagnetic Fe spin arrangement occurs below 130 K. In contrast, the magnetic domains are formed below 170 K and the average size of the magnetic domains was estimated as ~124 Å. These results explain the discrepancy of the Néel temperatures between three measurement techniques: magnetization, neutron powder diffraction and Mössbauer measurements. Furthermore, it was found that the magnetic domains coexist with the long-range antiferromagnetic ordering below 130 K.

The application of distance distribution functions to structural analysis of core–shell particles

Mykhaylyk, O.O. — 2007-04-21

The structure of core–shell latex particles of polymethylmethacrylate (the core) and polyurethane (the shell) have been investigated by methods of small-angle X-ray scattering (SAXS) and atom-force microscopy. A set of SAXS patterns has been obtained using contrast variation method. Indirect methods have been used to follow the evolution of distance distribution functions from SAXS for lattices in various sucrose solutions over a range of solution density, yielding structural parameters of the particles such as core size, shell thickness and density of the polymers including density deviations within the particle's core and shell. A model for an ensemble of core–shell particles with a normal distribution of average electron density of both the core and the shell has been developed to fit the distance distribution functions using a random search algorithm. The effects of nanophase separation in the polyurethane is estimated using Monte Carlo simulations of the distance distribution functions where the phase-separated polyurethane is represented by spherical truncated cones in a shell simulating the location of hard and soft polyurethane blocks, respectively.

Small-angle scattering studies of macromolecular solutions

Svergun, D.I. — 2007-04-21

In recent years, major progress has been achieved in developing novel approaches to interpret small-angle scattering data from solutions of biological macromolecules in terms of three-dimensional models. These advanced methods include: ab initio low-resolution shape and domain structure determination; modelling of quaternary structure by rigid-body refinement; simultaneous analysis of multiple scattering patterns, e.g. from contrast variation in neutron scattering to study multicomponent complexes; validation of high-resolution models; and addition of missing loops and domains. The new techniques will be presented and practical applications of the methods are illustrated by recent examples. The use of additional information from other methods, joint applications of X-ray and neutron scattering, and the possibilities for assessing and validating the models constructed based on small-angle scattering data will be discussed.

Reordering of magnetic colloid structures in external magnetic fields

Heinemann, A. — 2007-04-21

Field-induced local ordering within a cobalt-based magnetic colloid has been studied with polarized small-angle scattering by turning the direction of the external magnetic field. By analysing the nuclear–magnetic cross term we were able to separate the scattering contributions from dipolar chains and domains of pseudo-crystalline hexagonal arrangements. The magnetic moments were found to be aligned along the external magnetic field and to follow the change of the field direction. The observed variation of the particle moments must give rise to a rearrangement of the local hexagonal structure with respect to the new field direction to explain the scattering pattern. We confirm this by two-dimensional simultaneous least-squares fits for different Q ranges [where Q = 4\pi \sin (\theta) / \lambda, λ is the X-ray wavelength and 2θ is the scattering angle] with a model containing a core–shell particle form factor and a structure factor composed of Gaussian peaks and contributions from polydisperse cylinders.

Small-angle neutron scattering study of aqueous solutions of pentanediol and hexanediol

Székely, N.K. — 2007-04-21

Aqueous solutions of 1,2-pentanediol, 1,5-pentanediol, 1,2-hexanediol and 1,6-hexanediol have been studied by small-angle neutron scattering over a wide range of concentrations and temperatures. The structure of the solutions on the mesoscopic length scale, corresponding to the intermolecular distances, was analysed with the help of the Kirkwood–Buff formalism. 1,2-Hexanediol solutions exhibited a strong attractive diol–diol interaction, a weak diol–diol attraction was found for 1,6-hexanediol and 1,2-pentanediol, and an extremely weak diol–diol attraction was found in 1,5-pentanediol solutions. The general tendencies are the following: aggregation is stronger as the length of the hydrophobic hydrocarbon chain increases and the 1,2-diols exhibit much stronger attraction then the 1,\omega-diols. The temperature dependence of the aggregation is weak for the 1,2-diols but strong for the 1,\omega-diols, indicating in the latter case the hydrophobic character of the interaction.

Self-assembled films of hydrophobin protein HFBIII from Trichoderma reesei

Kisko, K. — 2007-04-21

Hydrophobins are a group of small amphiphilic proteins which are known to self-assemble on interfaces. They contain eight conserved cysteine residues, which make four disulfide bridges. A new hydrophobin protein, HFBIII, from the fungus Trichoderma reesei contains one extra cysteine residue, giving the protein a naturally reactive site. The self-assembly of hydrophobin protein HFBIII was studied using grazing-incidence X-ray diffraction and reflectivity. HFBIII self-assembles into a hexagonally ordered monolayer at an air/water interface and also forms crystalline coatings on a silicon substrate. The lattice constants for the hexagonal coatings are a = b = 56.5 Å, γ = 120°. The self-assembled structure in the HFBIII film is very similar to those formed by two other T. reesei hydrophobins, HFBI and HFBII.

Anomalous small- and wide-angle X-ray scattering and X-ray absorption spectroscopy for Pt and Pt–Ru nanoparticles

Jeng, U.-S. — 2007-04-21

We have characterized the structures of two kinds of catalytic nanoparticles of Pt and Pt–Ru, using anomalous small-angle X-ray scattering (ASAXS), anomalous wide-angle X-ray scattering (AWAXS) and extended X-ray absorption fine structure (EXAFS) spectroscopy. With several X-ray energies near the Pt LIII edge, the AWAXS data reveal a face-centered cubic (f.c.c.) crystalline structure for Pt nanoparticles supported on carbon black, whereas the ASAXS data characterize the monometallic nanoparticles as polydisperse spheres with a mean size of 23 Å and a size distribution of 20%. With similar X-ray energies, ASAXS and AWAXS data for the Pt–Ru nanoparticles indicate that they have a mean size of ~29 Å and a slightly Pt-rich core that can be characterized by an f.c.c. crystalline structure similar to that of the pure Pt nanoparticles. The coordination numbers of the bimetallic nanoparticles extracted from the EXAFS data, collected at the Pt LIII edge and Ru K edge, also reveal a consistent structure of largely, but not completely, intermixed Pt and Ru atoms in the nanoparticles.

Likelihood of crystallization: experimental and computational approaches

Carugo, O. — 2007-04-01

A report on the VIZIER Workshop on the `Definition of protein domains and their likelihood of crystallization', Vienna, Austria, 28–30 June 2006.

Reduction of two-dimensional small- and wide-angle X-ray scattering data

Boesecke, P. — 2007-04-21

At the beamlines ID01 and ID02 of the European Synchrotron Radiation Facility in Grenoble, France, position-sensitive detectors for time-resolved small- and wide-angle X-ray scattering experiments are in use. The applied data reduction method has never been described comprehensively. This article outlines the parametrization of the raw data and introduces the programs developed for this purpose. Data reduction in the sense of this article means all steps between detector readout and normalization to absolute scattering intensities. This includes all corrections that can be made without any specific knowledge of the sample, e.g. detector dark-image correction, division by a flat-field and intensity normalization. Processed data are either two- or one-dimensional. Optionally, statistical errors can be propagated through the calculations.

A comparison of methods for the measurement of the particle-size distribution of magnetic nanoparticles

Woodward, R.C. — 2007-04-21

Recently, interest in magnetic particles, particularly in the nanometre-size range, has increased significantly. The main driving forces behind this interest are both the development of improved synthesis techniques and an increase in the number of potential applications for suitable magnetic nanoparticles. A critical factor of interest in both the synthesis and the development of applications is the particle-size distribution. In this paper, we investigate three common techniques for determining the particle-size distribution of magnetic nanoparticles (electron microscopy, magnetic measurements and small-angle neutron scattering). We compare the distributions determined by each technique for two standard samples and discuss their advantages, disadvantages and limitations.

Small-angle X-ray scattering measurements of expanded fluid Se in the semiconductor–metal transition region using synchrotron radiation

Inui, M. — 2007-04-21

Small-angle X-ray scattering measurements for expanded fluid Se were carried out up to the semiconductor–metal transition region at high temperature and high pressure. A broad peak appears in the small-angle X-ray scattering profiles in the temperature range 1273 to 1773 K at 60 MPa, which suggests a correlation length of 50 Å. We fitted the patterns using a model function proposed by Teubner & Strey [J. Chem. Phys. (1987), 87, 3195–3200] and obtained two characteristic lengths, the domain size of the dense and rare regions, and the correlation length concerning their boundary. The present results suggest peculiar density fluctuations accompanying the SC-M transition in fluid Se consisting of polymeric molecules.

Synchrotron X-ray scattering studies on the structural evolution of microbial poly(3-hydroxybutyrate)

Heo, K. — 2007-04-21

The crystallization behavior of microbially synthesized poly(3-hydroxybutyrate) was studied in detail using time-resolved small-angle X-ray scattering. This polyester was found to undergo primary crystallization as well as secondary crystallization. In the primary crystallization, the thicknesses of the lamellar crystals were sensitive to the crystallization temperature, but no thickening was observed throughout the entire crystallization at a given temperature. The thickness of the lamellar crystals in the polyester was always larger than that of the amorphous layers. Secondary crystallization favorably occurred during the later stage of isothermal crystallization in competition with the continuous primary crystallization, forming secondary crystals in amorphous regions, in particular in the amorphous layers between the primarily formed lamellar crystal stacks. Compared to the primarily formed lamellar crystals, the secondary crystals had short-range-ordered structures of smaller size, a broader size distribution, and a lower electron density.

Effects of side-chain length on the magnetic response of discotic metallomesogens

Lee, J.-H. — 2007-04-21

The magnetic responses of columnar superstructures of discotic metallomesogens with different alkyl side-chain lengths, cobalt octa(n-alkylthio)porphyrazine (CoSx, where x is the peripheral n-alkyl chain length, x = 10, 12, 14), have been investigated by small-angle neutron scattering (SANS). CoSx (x = 10, 12, 14) were heated to their isotropic phases and cooled down to their columnar mesophases under various external magnetic fields (0.2–1.1 T) and the orientational orderings of the columnar mesophases were measured by SANS. The SANS patterns showed clear anisotropies indicating the alignment of columnar domains with their columnar directors perpendicular to the applied magnetic field. The annularly averaged SANS data, I(Φ), of CoSx (x = 10, 12, 14) under various magnetic field strengths were fitted with Lorentzian functions. The full width at half maximum (FWHM) of the I(Φ) of CoS10 and CoS12 rapidly decreases with increasing applied magnetic field and then saturates to about 42° at ~0.5 T and 50° at ~0.6 T, respectively. In the case of CoS14, however, the diffraction anisotropy was very weak even at field strengths as high as 1.13 T and the FWHM was very broad, ca. 120°. The dramatic decrease of magnetic field sensitivity of CoS14 may be attributed to the entropy increase with the side-chain length.

Density fluctuations in oxide glasses investigated by small-angle X-ray scattering

Levelut, C. — 2007-04-21

The structure of glasses is characterized by the existence of density and composition fluctuations on the nanometre scale. We present three examples of the use of small-angle X-ray scattering to get information about these density fluctuations. The thermal history and OH content were observed to have a huge influence. The static compressibility decreases when the OH content or fictive temperature increase. We showed that temperature scanning small-angle X-ray scattering can provide an accurate description of the position, width and shape of the glass transition.

Core structure of latent heavy-ion tracks in {100} LiF derived by small-angle X-ray scattering

Abu Saleh, S. — 2007-04-21

Radial electron densities within 27–111 µm-long ion damage trails, `latent ion tracks', created in {100} LiF by irradiation with GeV Pb and U projectiles, have been derived by means of small-angle X-ray scattering. The tracks exhibit continuous electron density decreases of 49–74% along the centers of their 2.3–3.4 nm-diameter cores. Structural alteration under the intense ion-deposited electronic excitation has been attributed to two successive processes: (a) local breakdown of the LiF lattice into fluorine molecules and Li atoms, and (b) release of the fluorine gas and of at least a portion of the voluminous Li atoms through the low-density tracks.