Open access article in Journal of Applied Crystallography

The current approach to initial crystallization screening of proteins is under-sampled

Gorrec, F. — 2013-06-01

Protein crystallization conditions that resulted in crystal structures published by scientists at the MRC Laboratory of Molecular Biology (MRC-LMB, Cambridge, UK) have been analysed. It was observed that the more often a crystallization reagent had been used to formulate the initial conditions, the more often it was found in the reported conditions that yielded diffraction quality crystals. The present analysis shows that, despite the broad variety of reagents, they have the same impact overall on the yield of crystal structures. More interestingly, the correlation implies that, although the initial crystallization screen may be considered very large, it is an under-sampled combinatorial approach.

CCL: an algorithm for the efficient comparison of clusters

Hundt, R. — 2013-06-01

The systematic comparison of the atomic structure of solids and clusters has become an important task in crystallography, chemistry, physics and materials science, in particular in the context of structure prediction and structure determination of nanomaterials. In this work, an efficient and robust algorithm for the comparison of cluster structures is presented, which is based on the mapping of the point patterns of the two clusters onto each other. This algorithm has been implemented as the module CCL in the structure visualization and analysis program KPLOT.

Development and applications of a new neutron single-crystal diffractometer based on a two-dimensional large-area curved position-sensitive detector

Lee, C.-H. — 2013-06-01

A new single-crystal neutron diffractometer based on a large-area curved two-dimensional position-sensitive detector (C-2DPSD) has been developed. The diffractometer commissioning is almost complete, together with development of the measurement methodology and the raw data processing software package, the Reciprocal Analyzer, and the instrument is now ready to be launched for users. Position decoding of the C-2DPSD is via a delay-line readout method with an effective angular range of 110 × 54° in the horizontal and vertical directions, respectively, with a nominal radius of curvature of 530 mm. The diffractometer is equipped with a Ge(311) mosaic monochromator and two supermirror vacuum guide paths, one before and one after the monochromator position. The commissioning incorporates corrections and calibration of the instrument using an NaCl crystal, various applications such as crystallographic and magnetic structure measurements, a crystallinity check on large crystals, and a study on the composition or dopant content of a mixed crystal of (TmxYb1−x)Mn2O5. The installation of the diffractometer and the measurement method, the calibration procedure and results, the raw data treatment and visualization, and several applications using the large C-2DPSD-based diffractometer are reported.

Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF

Monaco, S. — 2013-06-01

The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.

Improvements and considerations for size distribution retrieval from small-angle scattering data by Monte Carlo methods

Pauw, B.R. — 2013-04-01

Monte Carlo (MC) methods, based on random updates and the trial-and-error principle, are well suited to retrieve form-free particle size distributions from small-angle scattering patterns of non-interacting low-concentration scatterers such as particles in solution or precipitates in metals. Improvements are presented to existing MC methods, such as a non-ambiguous convergence criterion, nonlinear scaling of contributions to match their observability in a scattering measurement, and a method for estimating the minimum visibility threshold and uncertainties on the resulting size distributions.

Liesegang-like patterns of Toll crystals grown in gel

Gangloff, M. — 2013-04-01

Generating high-quality crystals remains a bottleneck in biological and materials sciences. Here a counter-diffusion method was used to improve the X-ray diffraction quality of the N-terminal domain of Drosophila melanogaster Toll receptor crystals. It was observed that crystallization occurred with a peculiar pattern along the capillary resembling Liesegang bands; this phenomenon is described at both macroscopic and atomic levels. It was found that bands appeared for native protein as well as for co-crystals of magic triangle (I3C)-bound protein even though they crystallize in different space groups. Crystallization occurred with a linear recurrence independent of the precipitant concentration and a protein-specific spacing coefficient. Bandwidth varied along the capillary, oscillating between large precipitation areas and single crystals. The reported data suggest that repetitive patterns can be generated with biological macromolecules in the presence of sodium malonate as a crystallization agent. A comparison with typical Liesegang patterns and the possible mechanism underlying this phenomenon are discussed.

Advanced Solid State Physics. By Philip Phillips. Pp. 402. 2nd ed. Cambridge University Press, 2012. Price (hardcover) GBP 45.00. ISBN 978-0-521-19490-7.

Eschrig, M. — 2013-02-01

Directional pair distribution function for diffraction line profile analysis of atomistic models

Leonardi, A. — 2013-02-01

The concept of the directional pair distribution function is proposed to describe line broadening effects in powder patterns calculated from atomistic models of nano-polycrystalline microstructures. The approach provides at the same time a description of the size effect for domains of any shape and a detailed explanation of the strain effect caused by the local atomic displacement. The latter is discussed in terms of different strain types, also accounting for strain field anisotropy and grain boundary effects. The results can in addition be directly read in terms of traditional line profile analysis, such as that based on the Warren–Averbach method.

Scherrer grain-size analysis adapted to grazing-incidence scattering with area detectors. Erratum

Smilgies, D.-M. — 2013-02-01

A poor divergence value in the paper by Smilgies [J. Appl. Cryst. (2009), 42, 1030–1034] is corrected.

The prolific polytypism of silicon carbide

Ortiz, A.L. — 2013-02-01

A worked example of polytypism is presented, aimed at assisting undergraduates in the learning and instructors in the teaching of this topic. In particular, this crystallography concept, not necessarily obvious for beginners, is illustrated pedagogically using to that end the model case of the prolific polytypism of silicon carbide (SiC). On the basis of concepts that are easily assimilated by students (i.e. simple topological constraints) this article first presents a unified description of the polytypism phenomenon in SiC that allows one to understand without difficulty the existence of its numerous polytypic variants and how they develop. Then the various notations used to designate these different polytypes are described, and finally the crystal structures of the most common are discussed. This worked example is thus expected to contribute to motivating undergraduates in the study of a crystallography topic that often is not treated in sufficient depth in class.

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

Classen, S. — 2013-02-01

The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B4C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.

Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals

Tanley, S.W.M. — 2013-02-01

The International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies and B factors of the bound Pt compounds. 35.3 Gb of data were transferred from Manchester to Utrecht to be processed with EVAL. A systematic comparison shows that the largest differences in the occupancies and B factors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets available via a local depository, it is possible for the diffraction community to make their own evaluation as they may wish.

A fast, simple and robust protocol for growing crystals in the lipidic cubic phase

Aherne, M. — 2012-12-01

A simple and inexpensive protocol for producing crystals in the sticky and viscous mesophase used for membrane protein crystallization by the in meso method is described. It provides crystals that appear within 15–30 min of setup at 293 K. The protocol gives the experimenter a convenient way of gaining familiarity and a level of comfort with the lipidic cubic mesophase, which can be daunting as a material when first encountered. Having used the protocol to produce crystals of the test protein, lysozyme, the experimenter can proceed with confidence to apply the method to more valuable membrane (and soluble) protein targets. The glass sandwich plates prepared using this robust protocol can further be used to practice harvesting and snap-cooling of in meso-grown crystals, to explore diffraction data collection with mesophase-embedded crystals, and for an assortment of quality control and calibration applications when used in combination with a crystallization robot.

Enhancing the volume and the optical quality of hen egg-white lysozyme crystals by coupling the salt concentration gradient crystallization method with a magnetic field

Magay, E. — 2012-10-01

The effect of coupling the salt concentration gradient crystallization method with the use of the paramagnetic salt MnCl2 and a magnetic field is reported. The use of a simple magnetic device is proposed to have a significant effect on hen egg-white lysozyme crystal growth. Large single crystals greater than 10 mm3 in volume with optical perfection were consistently obtained in this study.

Nonlinear Mechanics of Crystals. By John D. Clayton. Pp. 700. Dordrecht, Heidelberg, London, New York: Springer, 2011. Price (hardcover) Euros 169.95. ISBN-978-94-007-0349-0.

Paufler, P. — 2012-08-01

From patterns to space groups and the eigensymmetry of crystallographic orbits: a reinterpretation of some symmetry diagrams in IUCr Teaching Pamphlet No. 14

Suescun, L. — 2012-08-01

The space group of a crystal pattern is the intersection group of the eigensymmetries of the crystallographic orbits corresponding to the occupied Wyckoff positions. Polar space groups without symmetry elements with glide or screw components smaller than 1/2 do not contain characteristic orbits and cannot be realized in patterns (structures) made by only one crystallographic type of object (atom). The space-group diagram of the general orbit for this type of group has an eigensymmetry that corresponds to a special orbit in a centrosymmetric supergroup of the generating group. This fact is often overlooked, as shown in the proposed solution for Plates (i)–(vi) of IUCr Teaching Pamphlet No. 14, and an alternative interpretation is given.

Three-dimensional Bragg coherent diffraction imaging of an extended ZnO crystalThis article also forms part of a special issue dedicated to advanced diffraction imaging methods of materials, which will be published as a virtual special issue of the journal in 2012/2013.

Huang, X. — 2012-08-01

A complex three-dimensional quantitative image of an extended zinc oxide (ZnO) crystal has been obtained using Bragg coherent diffraction imaging integrated with ptychography. By scanning a 2.5 µm-long arm of a ZnO tetrapod across a 1.3 µm X-ray beam with fine step sizes while measuring a three-dimensional diffraction pattern at each scan spot, the three-dimensional electron density and projected displacement field of the entire crystal were recovered. The simultaneously reconstructed complex wavefront of the illumination combined with its coherence properties determined by a partial coherence analysis implemented in the reconstruction process provide a comprehensive characterization of the incident X-ray beam.

PROSPERO: online prediction of crystallographic success from experimental results and sequence

Zucker, F.H. — 2012-06-01

The growth of diffracting crystals from purified proteins is often a major bottleneck in determining structures of biological and medical interest. The PROSPERO web server, http://skuld.bmsc.washington.edu/prospero, is intended both to provide a means of organizing the potentially large numbers of experimental characterizations measured from such proteins, and to provide useful guidance for structural biologists who have succeeded in purifying their target protein but have reached an impasse in the difficult and poorly understood process of turning purified protein into well diffracting crystals. These researchers need to decide which of many possible rescue options are worth pursuing, given finite resources. This choice is even more crucial when attempting to solve high-priority but relatively difficult structures of eukaryotic proteins. The site currently uses the HyGX1 predictor, which was trained and validated on protein samples from pathogenic protozoa (eukaryotes) using results from six types of experiment. PROSPERO allows users to store, analyze and display multiple results for each sample, to group samples into projects, and to share results and predictions with collaborators.

Graphical tools for macromolecular crystallography in PHENIX

Echols, N. — 2012-06-01

A new Python-based graphical user interface for the PHENIX suite of crystallography software is described. This interface unifies the command-line programs and their graphical displays, simplifying the development of new interfaces and avoiding duplication of function. With careful design, graphical interfaces can be displayed automatically, instead of being manually constructed. The resulting package is easily maintained and extended as new programs are added or modified.

Valentin Ivanovich Simonov (1930–2012)

Group of colleagues — 2012-06-01

Materials Science of DNA. Edited by J.-I. Jin and J. Grote. Pp. 326. Boca Raton: CRC Press, Taylor & Francis Group, 2012. Price (hardcover) GBP 76.99. ISBN 978-1-398-2741-3.

Pompe, W. — 2012-06-01

Hans Dachs (1927–2011)

Steiner, M. — 2012-04-01

Introduction to Nonlinear Optics. By Geoffrey New. Pp. xv+257. Cambridge: University Press, 2011. Price (hardcover) GBP 45.00, USD 75.00. ISBN-9780521877015.

Paufler, P. — 2012-06-01

CrystalEye: automated aggregation, semantification and dissemination of the world's open crystallographic data

Day, N. — 2012-04-01

CrystalEye automatically aggregates crystallographic data from web resources (the supplementary data to articles on publishers' web sites) into a structured XML-based repository, and then adds value to that open data by providing methods to easily browse, search and to keep up-to-date with the latest published information.

Alexander McLeod Mathieson (1920–2011)

Wilkins, S. — 2012-04-01

Crystal Engineering. A Textbook. By Gautam R. Desiraju, Jagadese J. Vittal and Arunachalam Ramanan. Pp. xiv+216. Singapore: World Scientific, 2011. Price (paperback) USD 49. ISBN-978 981 4366 86 1.

Paufler, P. — 2012-04-01

A simplified invariant line analysis for face-centred cubic/body-centred cubic precipitation systems. Erratum

Liu, H. — 2012-02-01

Errors in the paper by Liu, Waclawik & Luo [J. Appl. Cryst. (2010), 43, 448–454] are corrected.

A manual low-cost protein-crystallization plate jig for in situ diffraction in the home laboratory

Hargreaves, D. — 2012-02-01

A prototype jig to attach a protein crystallization plate to a standard X-ray goniometer has been designed and constructed in partnership with an engineering firm. This allows a low-cost implementation of in situ diffraction using the available home-laboratory X-ray source.

Concepts and Methods of 2D Infrared Spectroscopy. By Peter Hamm and Martin Zanni. Pp. 296, 124 illustrations, 71 exercises. Cambridge University Press, 2011. Price (hardcover) 99.00 USD. ISBN 978-1-107-00005-6.

Vtyurin, A. — 2012-02-01

ShelXle: a Qt graphical user interface for SHELXL

Hübschle, C.B. — 2011-12-01

ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

ANODE: anomalous and heavy-atom density calculation

Thorn, A. — 2011-12-01

The new program ANODE estimates anomalous or heavy-atom density by reversing the usual procedure for experimental phase determination by methods such as single- and multiple-wavelength anomalous diffraction and single isomorphous replacement anomalous scattering. Instead of adding a phase shift to the heavy-atom phases to obtain a starting value for the native protein phase, this phase shift is subtracted from the native phase to obtain the heavy-atom substructure phase. The required native phase is calculated from the information in a Protein Data Bank file of the structure. The resulting density enables even very weak anomalous scatterers such as sulfur to be located. Potential applications include the identification of unknown atoms and the validation of molecular replacement solutions.

iotbx.cif: a comprehensive CIF toolbox

Gildea, R.J. — 2011-12-01

iotbx.cif is a new software module for the development of applications that make use of the CIF format. Comprehensive tools are provided for input, output and validation of CIFs, as well as for interconversion with high-level cctbx [Grosse-Kunstleve, Sauter, Moriarty & Adams (2002). J. Appl. Cryst. 35, 126–136] crystallographic objects. The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language.

Le cristal et ses doubles. By Jean-Claude Boulliard. Pp. 347. Paris: CNRS Éditions, 2010. In French. Price (hardcover) EUR 59. ISBN 978-2-271-07049-4.

Klapper, H. — 2011-12-01

Supercritical carbon dioxide behaviour in porous silica aerogel. Erratum

Ciccariello, S. — 2011-10-01

Errors in the paper by Ciccariello, Melnichenko & He [J. Appl. Cryst. (2011), 44, 43–51] are corrected.

Simon Charles Moss (1934–2011)

Schönfeld, B. — 2011-08-01

Combined Analysis. By D. Chateigner. Pp. xviii + 497, 188 figures + 46 tables. London, Hoboken: ISTE Ltd, Wiley, 2010. Price (hardcover) EUR 132. ISBN 978-1-84821-198-8.

Esling, C. — 2011-08-01

New software for statistical analysis of Cambridge Structural Database data

Sykes, R.A. — 2011-08-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments.

CIFXML: a schema and toolkit for managing CIFs in XML

Day, N.E. — 2011-06-01

CIFXML applies the XML strategies and technologies to create a general interface for processing CIF documents that conform to the CIF syntax and DDL1. Both a DTD and an XML schema for CIFs are presented. CIFs can be read, edited, validated syntactically, sorted, normalized, filtered, stored as an XML document object model, transformed and output. CIFXOM provides an easy way of converting CIFs to XML and vice versa using Java.

Incoherent neutron scattering from multi-element materials

Glinka, C.J. — 2011-06-01

In a neutron diffraction measurement, including small-angle scattering, there is generally a featureless (i.e. Q-independent) component due to incoherent scattering. This scattering contains no information about the atomic structure or structure on any scale. There may also be featureless scattering that arises from atomic disorder in multi-element materials. This scattering is sometimes referred to as compositional or mixture incoherent scattering. However, this designation is misleading. A much better designation is diffuse coherent scattering. Here the differences and distinguishing characteristics of incoherent scattering vis-à-vis diffuse coherent scattering due to atomic disorder are delineated and demonstrated experimentally.

Evaluation of the Bruker SMART X2S: crystallography for the nonspecialist?

Eccles, K.S. — 2011-02-01

An evaluation of the Bruker SMART X2S for the collection of crystallographic diffraction data, structure solution and refinement is carried out with a variety of materials with different electron densities, presenting some of the successes and challenges of automation in chemical crystallography.

MoleCoolQt – a molecule viewer for charge-density research

Hübschle, C.B. — 2011-02-01

MoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for example, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso, color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms – as sometimes required for local atomic coordinate systems – are calculated on demand; XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD, MoPro, SHELX, GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS.

Versatile in situ powder X-ray diffraction cells for solid–gas investigations

Jensen, T.R. — 2010-12-01

This paper describes new sample cells and techniques for in situ powder X-ray diffraction specifically designed for gas absorption studies up to ca 300 bar (1 bar = 100 000 Pa) gas pressure. The cells are for multipurpose use, in particular the study of solid–gas reactions in dosing or flow mode, but can also handle samples involved in solid–liquid–gas studies. The sample can be loaded into a single-crystal sapphire (Al2O3) capillary, or a quartz (SiO2) capillary closed at one end. The advantages of a sapphire single-crystal cell with regard to rapid pressure cycling are discussed, and burst pressures are calculated and measured to be ∼300 bar. An alternative and simpler cell based on a thin-walled silicate or quartz glass capillary, connected to a gas source via a VCR fitting, enables studies up to ∼100 bar. Advantages of the two cell types are compared and their applications are illustrated by case studies.

A general method to determine twinning elements

Zhang, Y. — 2010-12-01

The fundamental theory of crystal twinning has been long established, leading to a significant advance in understanding the nature of this physical phenomenon. However, there remains a substantial gap between the elaborate theory and the practical determination of twinning elements. This paper proposes a direct and simple method – valid for any crystal structure and based on the minimum shear criterion – to calculate various twinning elements from the experimentally determined twinning plane for Type I twins or the twinning direction for Type II twins. Without additional efforts, it is generally applicable to identify and predict possible twinning modes occurring in a variety of crystalline solids. Therefore, the present method is a promising tool to characterize twinning elements, especially for those materials with complex crystal structure.

Lachlan M. D. Cranswick (1968–2010)

Scarlett, N. — 2010-10-01

RapiData: a practical course in macromolecular X-ray diffraction data measurement and structure solving at the NSLS

Sweet, R.M. — 2010-10-01

RapiData provides two days of high-level lectures, then two more of experimental work on several beamlines of the National Synchrotron Light Source, for about 50 students. Students are invited to bring their own research projects for measurement, and about half of them do. The students frequently solve half a dozen structures during the course. Tutorials by the lecturers run throughout the data-collection period. The crystal-preparation laboratory is popular for tutorials and practice, and often there is a beamline available for practice. This article provides details about the organization of the course and tells some of the reasons for its success.

Crystallography education and training for the 21st century

Kantardjieff, K.A. — 2010-10-01

Observations on online educational materials for powder diffraction crystallography software

Toby, B.H. — 2010-10-01

This article presents a series of approaches used to educate potential users of crystallographic software for powder diffraction. The approach that has been most successful in the author's opinion is the web lecture, where an audio presentation is coupled to a video-like record of the contents of the presenter's computer screen.

Jmol – a paradigm shift in crystallographic visualization

Hanson, R.M. — 2010-10-01

Recent advances in molecular and crystallographic visualization methods are allowing instructors unprecedented opportunities to enhance student learning using virtual models within a familiar web-browser context. In step with these advances, the latest versions of the Jmol molecular visualization applet offer capabilities that hold potential for revolutionizing the way students learn about symmetry, uncertainty and the overall enterprise of molecular structure determination.

Teaching crystallography to undergraduate physical chemistry students

Pett, V.B. — 2010-10-01

Teaching goals, laboratory experiments and homework assignments are described for teaching crystallography as part of two undergraduate physical chemistry courses. A two-week teaching module is suggested for introductory physical chemistry, including six to eight classroom sessions, several laboratory experiences and a 3 h computer-based session, to acquaint undergraduate physical chemistry students with crystals, diffraction patterns, the mathematics of structure determination by X-ray diffraction, data collection, structure solution and the chemical insights available from crystal structure information. Student projects and laboratory work for three to four weeks of an advanced physical chemistry course are presented. Topics such as symmetry operators, space groups, systematic extinctions, methods of solving the phase problem, the Patterson map, anomalous scattering, synchrotron radiation, crystallographic refinement, hydrogen bonding and neutron diffraction all lead to the goal of understanding and evaluating a crystallographic journal article. Many of the ideas presented here could also be adapted for inorganic chemistry courses.

Update on the tutorial for learning and teaching macromolecular crystallography

Faust, A. — 2010-10-01

Two new experiments (single isomorphous replacement including anomalous-scattering effects and radiation damage-induced phasing) have been designed to complement the five experiments (sulfur single-wavelength anomalous diffraction, multiple-wavelength anomalous diffraction, molecular replacement, ion binding and ligand binding) of the first edition of the previously described tutorial for learning and teaching macromolecular crystallography [Faust, Panjikar, Mueller, Parthasarathy, Schmidt, Lamzin & Weiss (2008). J. Appl. Cryst. 41, 1161–1172]. Furthermore, the tutorial has been re-organized and in part re-written to reflect the comments and suggestions of users. The most significant overhaul was applied to the data-processing part of the tutorial. Nevertheless, the convenient features that all of the utilized proteins used are commercially available and that they can be easily and reproducibly crystallized and mounted for diffraction data collection have been retained. Also, for all of the seven experiments the raw diffraction images and the processed data are provided for illustrating and teaching the steps of data processing and structure determination.

Teaching general chemistry, solid-state chemistry and crystallography in one comprehensive undergraduate course: can the effect be synergistic?

Boldyreva, E. — 2010-10-01

This contribution describes a 30-year experience of teaching a general course in solid-state chemistry for undergraduates, which introduces at the same time the main concepts of crystallography, gives an introduction to structure analysis techniques, and makes links to courses in inorganic chemistry, organic chemistry and biochemistry. Such a combination can be beneficial for bringing the fundamentals of crystallography (basics and techniques) closer to its `users' – chemists, materials scientists, biologists – and can be considered as an attempt to create a course in `applied crystallography'. The aim of the course is to teach chemists which chemical information can be retrieved from a crystal structure and how. This is complementary to more generally accepted courses, which teach how to obtain structural information and to describe crystal structures.

Crystal cookery – using high-throughput technologies and the grocery store as a teaching tool

Luft, J.R. — 2010-10-01

Crystallography is a multidisciplinary field that links divergent areas of mathematics, science and engineering to provide knowledge of life on an atomic scale. Crystal growth, a key component of the field, is an ideal vehicle for education. Crystallization has been used with a `grocery store chemistry' approach and linked to high-throughput remote-access screening technologies. This approach provides an educational opportunity that can effectively teach the scientific method, readily accommodate different levels of educational experience, and reach any student with access to a grocery store, a post office and the internet. This paper describes the formation of the program through the students who helped develop and prototype the procedures. A summary is presented of the analysis and preliminary results and a description given of how the program could be linked with other aspects of crystallography. This approach has the potential to bridge the gap between students in remote locations and with limited funding, and access to scientific resources, providing students with an international-level research experience.

Pushing the boundaries of technology to educate and train the next generation of crystallographers

Kantardjieff, K. — 2010-10-01

This article describes the evolution of educational technologies, moving from the Web 1.0 to the current Web 3.0 decade, with the aim of stimulating discussion and inspiring innovative and effective crystallography education in the Web 3.0 decade. In the last 15 years, academic crystallography has largely migrated from a research specialty to a technique employed by a broad user community. This has led to the growth of and dependence on independently funded workshops and summer schools, as well as other non-traditional curricular resources for crystallography instruction, such as web pages and online courses, which allow crystallography to be self-taught. In fact, informal courses and e-learning constitute 70–80% of all learning today, and students expect on-demand learning. Implementing modern web technologies with sound pedagogy requires skilful integration of relevant, often disparate, resources into useful and usable frameworks, enabling learners to interact, explore new situations, and use scientific reasoning skills such as hypothesis testing and model-based reasoning. The evident disproportion in implementing contemporary technologies into our global crystallography education resources requires that we shift our focus from simply imparting subject knowledge by posting largely text-based content to empowering students with the fundamental processes and skills needed for on-demand learning and practice in crystallography.

Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system

Gerdts, C.J. — 2010-10-01

The Microcapillary Protein Crystallization System (MPCS) is a microfluidic, plug-based crystallization technology that generates X-ray diffraction-ready protein crystals in nanolitre volumes. In this study, 28 out of 29 (93%) proteins crystallized by traditional vapor diffusion experiments were successfully crystallized by chemical gradient optimization experiments using the MPCS technology. In total, 90 out of 120 (75%) protein/precipitant combinations leading to initial crystal hits from vapor diffusion experiments were successfully crystallized using MPCS technology. Many of the resulting crystals produced high-quality X-ray diffraction data, and six novel protein structures that were derived from crystals harvested from MPCS CrystalCards are reported.

Scientific inquiry, inference and critical reasoning in the macromolecular crystallography curriculum

Rupp, B. — 2010-10-01

The astounding progress in methods and technology that led to the undisputed success and impact of biomolecular crystallography on areas ranging from essential structural biology to therapeutic drug discovery or the study of molecular complexes of ever increasing size and beauty has brought with it new requirements for the education of students in the field. With the great power of modern crystallography comes great responsibility for its appropriate use, and a modern curriculum must extend beyond the delivery of required technical expertise. The complexity of macromolecular models and the sometimes low determinacy, combined with local variety in structure quality, requires that the student is provided with means of critical analysis and hypothesis testing that extend beyond classical validation, developing a mindset that remains robust against mental bias towards finding what one seeks. The increasing neglect of critical analysis and hypothesis testing in many undergraduate curricula requires that the modern crystallography curriculum itself addresses such fundamental analytical tools of the scientific method to avoid high-profile structure retractions that might tarnish the otherwise unrivalled contributions of macromolecular crystallography to our understanding of the molecular basis of life.

How to read (and understand) Volume A of International Tables for Crystallography: an introduction for nonspecialists

Dauter, Z. — 2010-10-01

Since fewer and fewer students get proper crystallographic education at the undergraduate level, the responsibility to promote and propagate this knowledge must be directed to alternative channels. It is not a marginal issue, because the language of crystallography is rather hermetic and, without proper support, it might disappear from the collective scientific knowledge, so that in the next generation there would be no-one able to use it properly, to say nothing about advancing the field. Black-box crystallography might be useful in some situations, but it cannot replace well informed, conscious scientific pursuits by properly trained specialists. Without sufficient understanding of crystallographic terms and principles, the now thriving branch of structural research would wither, and this could have particularly lamentable consequences for structural biology. The purpose of this article is to teach non-initiated persons, primarily structural biologists, how to interpret the information contained in the fundamental Volume A of International Tables for Crystallography (ITA). An excellent and comprehensive overview of many issues concerning crystal symmetry is presented in a book by Burns & Glazer (Space Groups for Solid State Scientists, 2nd ed. New York: Academic Press, 1990), also explaining the contents of ITA, but this text is unfortunately not popular among structural biologists. There are several superb handbooks explaining the foundations of structural crystallography but they usually do it without direct reference to ITA. There is also a comprehensive introduction included in ITA, but it is written in rather hermetic language and is, therefore, not suitable for nonspecialists with no training in exact sciences. This article, which uses simple language to explain all the terms encountered on the space-group pages of ITA, is meant to bridge this growing gap in crystallographic instruction. The explanations are illustrated with actual examples taken directly from the pages of ITA.

Remote access to crystallography beamlines at SSRL: novel tools for training, education and collaboration

Smith, C.A. — 2010-10-01

For the past five years, the Structural Molecular Biology group at the Stanford Synchrotron Radiation Lightsource (SSRL) has provided general users of the facility with fully remote access to the macromolecular crystallography beamlines. This was made possible by implementing fully automated beamlines with a flexible control system and an intuitive user interface, and by the development of the robust and efficient Stanford automated mounting robotic sample-changing system. The ability to control a synchrotron beamline remotely from the comfort of the home laboratory has set a new paradigm for the collection of high-quality X-ray diffraction data and has fostered new collaborative research, whereby a number of remote users from different institutions can be connected at the same time to the SSRL beamlines. The use of remote access has revolutionized the way in which scientists interact with synchrotron beamlines and collect diffraction data, and has also triggered a shift in the way crystallography students are introduced to synchrotron data collection and trained in the best methods for collecting high-quality data. SSRL provides expert crystallographic and engineering staff, state-of-the-art crystallography beamlines, and a number of accessible tools to facilitate data collection and in-house remote training, and encourages the use of these facilities for education, training, outreach and collaborative research.

Lodovico Riva Di Sanseverino (1939–2010)

Mealli, C. — 2010-08-01

Applications of the Cambridge Structural Database in chemical educationThis paper is part of a short series celebrating the archiving of the 500 000th crystal structure to the Cambridge Structural Database in November 2009.

Battle, G.M. — 2010-10-01

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

The Bravais polar lattice as a didactic tool for diffraction beginners

Nespolo, M. — 2010-10-01

When undergraduate students discover crystallography for the first time, they are usually already familiar with the phenomenon of diffraction as the `bending' of waves around small obstacles. The special (periodic) nature of crystals acting as `diffraction gratings' that produce interference of diffracted waves is typically rationalized in terms of the reciprocal lattice of the crystal. The concept of the reciprocal lattice, however, remains somewhat abstract for beginners, until they perform a diffraction experiment. It can be made more easily understandable through an intermediate step, namely its ancestor, the Bravais polar lattice. By means of a short historical trip through pre-X-ray crystallography, a generalized introduction to the notion of the dual lattice is given, of which the reciprocal lattice is the most common but by no means the only example, and it is shown how the use of the Bravais polar lattice can ease the introduction of the reciprocal lattice.

Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences

Dutta, S. — 2010-10-01

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education worldwide by providing an essential resource of information on biomolecular structures. In addition to serving as a deposition, data-processing and distribution center for PDB data, the RCSB PDB offers resources and online materials that different audiences can use to customize their structural biology instruction. These include resources for general audiences that present macromolecular structure in the context of a biological theme, method-based materials for researchers who take a more traditional approach to the presentation of structural science, and materials that mix theme-based and method-based approaches for educators and students. Through these efforts the RCSB PDB aims to enable optimal use of structural data by researchers, educators and students designing and understanding experiments in biology, chemistry and medicine, and by general users making informed decisions about their life and health.

The extended Q-range small-angle neutron scattering diffractometer at the SNS

Zhao, J.K. — 2010-10-01

The extended Q-range small-angle neutron scattering diffractometer (EQ-SANS) at the Spallation Neutron Source (SNS), Oak Ridge, is designed for wide neutron momentum transfer (Q) coverage, high neutron beam intensity and good wavelength resolution. In addition, the design and construction of the instrument aim to achieve a maximum signal-to-noise ratio by minimizing the background. The instrument is located on the high-power target station at the SNS. One of the key components in the primary flight path is the neutron optics, consisting of a curved multichannel beam bender and sections of straight neutron guides. They are optimized to minimize neutron transport loss, thereby maximizing the available flux on the sample. They also enable the avoidance of a direct line of sight to the neutron moderator at downstream locations. The instrument has three bandwidth-limiting choppers. They allow a novel frame-skipping operation, which enables the EQ-SANS diffractometer to achieve a dynamic Q range equivalent to that of a similar machine on a 20 Hz source. The two-dimensional low-angle detector, based on 3He tube technologies, offers very high counting rates and counting efficiency. Initial operations have shown that the instrument has achieved its design goals.

publCIF: software for editing, validating and formatting crystallographic information files

Westrip, S.P. — 2010-08-01

publCIF is an application designed for creating, editing and validating crystallographic information files (CIFs) that are used in journal publication. It validates syntax and dictionary-defined data attributes through internal routines, and also provides a web interface to the checkCIF service of the International Union of Crystallography (IUCr), which provides a full crystallographic analysis of the structural data. The graphical interface allows users to edit the CIF either in its `raw' ASCII form (using a text editor with context-sensitive data validation and input facilities) or as a formatted representation of a structure report (using a word-processing environment), as well as via a number of convenience tools (e.g. spreadsheet representations of looped data). Beyond file and data validation, publCIF provides access to resources to facilitate preparation of a structure report (e.g. databases of author details, experimental data, standard references etc., either distributed with the program or collected during its use), along with tools for reference parsing, spell checking, structure visualization and image management. publCIF was commissioned by the IUCr, both as free software for authors and as a tool for in-house journal production; the tool for authors is described here. Binary distributions for Linux, MacOS and Windows operating systems are available.

Gerard Rieck (1911–2010)

Metselaar, R. — 2010-08-01

ASTAR: a .NET class library for STAR/CIF manipulation

Lin, Y. — 2010-08-01

A .NET class library for STAR/CIF manipulation, ASTAR, has been developed and is available at http://xstar.sourceforge.net/astar/. The library provides facilities to read and write STAR/CIF files and an object model to manipulate data in STAR/CIF files. While the library is written in the C# programming language, it can be utilized by programs written in various programming languages targeting the .NET platform.

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

Afonine, P.V. — 2010-08-01

phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available shows that in most cases the reported statistics, in particular R factors, can be reproduced within a few percentage points. However, there are a number of outliers where the recomputed R values are significantly different from those originally reported. The reasons for these discrepancies are discussed.

Introduction to texture analysis: macrotexture, microtexture and orientation mapping. By Olaf Engler and Valerie Randle. Pp. 456. 2nd ed. Boca Raton: CRC Press, 2010. Price (paperback) USD 129.95. ISBN 978-1-4200-6365-3.

Skrotzki, W. — 2010-08-01

Autoindexing with outlier rejection and identification of superimposed lattices

Sauter, N.K. — 2010-06-01

Constructing a model lattice to fit the observed Bragg diffraction pattern is straightforward for perfect samples, but indexing can be challenging when artifacts are present, such as poorly shaped spots, split crystals giving multiple closely aligned lattices and outright superposition of patterns from aggregated microcrystals. To optimize the lattice model against marginal data, refinement can be performed using a subset of the observations from which the poorly fitting spots have been discarded. Outliers are identified by assuming a Gaussian error distribution for the best-fitting spots and points diverging from this distribution are culled. The set of remaining observations produces a superior lattice model, while the rejected observations can be used to identify a second crystal lattice, if one is present. The prevalence of outliers provides a potentially useful measure of sample quality. The described procedures are implemented for macromolecular crystallography within the autoindexing program labelit.index (http://cci.lbl.gov/labelit).

The mystery of the giant crystals. A film directed by Javier Trueba. Written and presented by Juan Manual García Ruiz. Madrid Scientific Films, 2010. Cat No. HR5-208. Duration 110 min. Format: HD (16:9). Available on DVD and Blu-Ray. Price USD 18.

Mühlberg, M. — 2011-06-01

Two-dimensional X-ray diffraction. By Bob Baoping He. Pp. 426. Hoboken: Wiley, 2009. Price (hardcover) GBP 76.95. ISBN 978-0-470-22722-0.

Massa, W. — 2010-06-01

Efforts to enhance coverage of crystallography in United States secondary education

Kantardjieff, K.A. — 2010-10-01

Because crystallography has often been regarded as an `experts only' science, requiring advanced mathematics and physics, it has been eliminated from many science curricula. In the United States, high school is a critical time when students are exposed to science at a more significant level, preparing them for university, and it is when they make career choices. A contemporary secondary science teaching credential must qualify teachers to present topics in substantive ways, to attract talented and enthusiastic young people to science, and to develop scientific literacy in the future workforce. Education and training policies put forward by the United States National Committee for Crystallography and the American Crystallographic Association recommend that molecular structure awareness should begin in K-12 (kindergarten through 12th grade) education as a core component for implementing established national science standards. Furthermore, many contexts exist in which crystallography can be incorporated into secondary education with minimal disruption. Following these guidelines, preparation of secondary teachers should include professional development in crystallography, providing them with knowledge (fundamental and practical), learning units, tools and modern examples to incorporate into their curricula. This article describes activities whose objective is to enhance secondary education by raising crystallography awareness through workshops, summer schools, student/teacher research internships and remote-enabling technologies.

Morphology of polysorbate 80 (Tween 80) micelles in aqueous dimethyl sulfoxide solutions

Aizawa, H. — 2010-06-01

The structures of micelles of the surfactant polysorbate 80 (Tween 80) in 0–50% aqueous dimethyl sulfoxide (DMSO) solutions (pH 7.2, ionic strength 2.44 mM) were investigated by means of small-angle X-ray scattering. At DMSO concentrations of 0–20%, core–shell cylinder micelles formed, and at 30–50% DMSO, core–shell discus micelles formed, that is, changing the hydrophobicity of the DMSO solvent mixture changed the micelles from core–shell cylinder micelles to core–shell discus micelles.

Aaron Joseph Kalb (Gilboa) (1937–2009)

Helliwell, J.R. — 2010-06-01

Biomolecular crystallography: principles, practice and applications to structural biology. By Bernhard Rupp. Pp. 808. Abingdon, New York: Garland Science, Taylor & Francis Group, 2010. Price (hardcover) USD 145.00. ISBN 9780815340812. ISBN-10 0815340818.

Blundell, T. — 2010-10-01

WebCSD: the online portal to the Cambridge Structural Database

Thomas, I.R. — 2010-04-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer.

Development of a shutterless continuous rotation method using an X-ray CMOS detector for protein crystallography

Hasegawa, K. — 2009-12-01

A new shutterless continuous rotation method using an X-ray complementary metal-oxide semiconductor (CMOS) detector has been developed for high-speed, precise data collection in protein crystallography. The principle of operation and the basic performance of the X-ray CMOS detector (Hamamatsu Photonics KK C10158DK) have been shown to be appropriate to the shutterless continuous rotation method. The data quality of the continuous rotation method is comparable to that of the conventional oscillation method using a CCD detector and, furthermore, the combination with fine ϕ slicing improves the data accuracy without increasing the data-collection time. The new method is more sensitive to diffraction intensity because of the narrow dynamic range of the CMOS detector. However, the strong diffraction spots were found to be precisely measured by recording them on successive multiple images by selecting an adequate rotation step. The new method has been used to successfully determine three protein structures by multi- and single-wavelength anomalous diffraction phasing and has thereby been proved applicable in protein crystallography. The apparatus and method may become a powerful tool at synchrotron protein crystallography beamlines with important potential across a wide range of X-ray wavelengths.

The MORPHEUS protein crystallization screen

Gorrec, F. — 2009-12-01

A 96-condition initial screen for protein crystallization, called MORPHEUS, has been developed at the MRC Laboratory of Molecular Biology, Cambridge, England (MRC-LMB). The concept integrates several innovative approaches, such as chemically compatible mixes of potential ligands, new buffer systems and precipitant mixes that also act as cryoprotectants. Instead of gathering a set of crystallization conditions that have already been successful, a selection of molecules frequently observed in the Protein Data Bank (PDB) to co-crystallize with proteins has been made. These have been put together in mixes of similar chemical behaviour and structure, and combined with buffers and precipitant mixes that were also derived from PDB searches, to build the screen de novo. Observations made at the MRC-LMB and many practical aspects were also taken into account when formulating the screen. The resulting screen is easy to use, comprehensive yet small, and has already yielded a list of crystallization hits using both known and novel samples. As an indicator of success, the screen has now become one of the standard screens used routinely at the MRC-LMB when searching initial crystallization conditions for biological macromolecules.

Automatic multiple-zone rigid-body refinement with a large convergence radius

Afonine, P.V. — 2009-08-01

Rigid-body refinement is the constrained coordinate refinement of one or more groups of atoms that each move (rotate and translate) as a single body. The goal of this work was to establish an automatic procedure for rigid-body refinement which implements a practical compromise between runtime requirements and convergence radius. This has been achieved by analysis of a large number of trial refinements for 12 classes of random rigid-body displacements (that differ in magnitude of introduced errors), using both least-squares and maximum-likelihood target functions. The results of these tests led to a multiple-zone protocol. The final parameterization of this protocol was optimized empirically on the basis of a second large set of test refinements. This multiple-zone protocol is implemented as part of the phenix.refine program.

Morphology of polysorbate 80 (Tween 80) micelles in aqueous 1,4-dioxane solutions

Aizawa, H. — 2009-08-01

The structures of micelles of the surfactant polysorbate 80 (Tween 80) in 0–50% aqueous 1,4-dioxane solutions (pH 7.2, ionic strength 2.44 mM) were investigated by means of small-angle X-ray scattering. At 1,4-dioxane concentrations of 0–20%, core–shell cylindrical micelles formed because the crown-shaped polysorbate 80 molecules aggregated into a cylindrical layer of four chains entangled with one another through intra- and intermolecular interactions. At 30–40% 1,4-dioxane, core–shell discus micelles formed, and at 50% 1,4-dioxane, core–shell elliptic discus micelles formed by the same mechanism. By changing the 1,4-dioxane solvent concentration and increasing the solvent hydrophobicity, the micelles first change from core–shell cylindrical to core–shell discus and then from core–shell discus to core–shell elliptic discus micelles.

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.

Richard J. Weiss (1923–2008)

Cooper, M.J. — 2009-06-01

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.

Dominique Grebille (1957–2009)

Pérez, O. — 2009-06-01

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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%.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Cylindrical nanochannels in ion-track polycarbonate membranes studied by small-angle X-ray scattering

Pépy, G. — 2007-04-21

Different types of polycarbonate foils were irradiated with 1.4 GeV Xe ions, ultra-violet (UV) treated and subsequently etched, creating cylindrical pores of high aspect ratio. The pores are perfectly well aligned and represent excellent objects for small-angle X-ray scattering. Two-dimensional scattering spectra exhibit highly anisotropic patterns with clear presentation of numerous oscillations of the Bessel function, the radial part of the scattering function. Modelling the pores as parallel cylinders allows us to deduce the pore radius and the radius dispersion as a function of UV treatment, etching time and fluence. It is demonstrated that the UV treatment has a beneficial influence on the pore-size distribution, in particular for small pores.

Green thin polymer film metallization using supercritical carbon dioxide

Koga, T. — 2007-04-21

It is shown that low-density polymer layers created by supercritical carbon dioxide (scCO2) processing can be exploited to enhance metallization of thin polymer films. Spun-cast thin films were exposed to scCO2 within the narrow temperature and pressure regime known as the `density fluctuation ridge', where excess swelling of the polymer thin films was induced, and the swollen structures could be subsequently preserved by quick evaporation of CO2. X-ray reflectivity (XR) measurements proved that the `expanded' films had a broader interfacial width between the polymer and deposited metal layers, regardless of the polymer film thickness or choice of polymers. Furthermore, standard peel test showed a drastic enhancement in adhesion between the polymer and metal layers, which correlates with the XR result: the broader interfacial width indicates increased adhesion.

Polymer dynamics: from synthetic polymers to proteins

Richter, D. — 2007-04-21

In polymeric materials, the structures, the macroscopic mechanical and rheological properties, and the phase changes are determined to a high degree by thermal motion of the atoms and molecules. Most of the relevant dynamics take place on mesoscopic lengths and timescales in between the picosecond atomic scale and the macroscopic frame. Offering the proper space–time observation window, neutron spin echo spectroscopy uniquely addresses these motions. We briefly present some key experimental results on the mesoscopic dynamics of polymer systems. We address briefly the standard model of polymer motion, the Rouse model, the role of topological confinement as expressed in the reptation model and, finally, processes limiting the confinement – we discuss contour length fluctuations and constraint release of entangled chains. Very recently it also became possible to directly identify large-scale internal dynamics of proteins by neutron spin echo. We report the results of these pioneering studies, which are most likely to initiate further experiments on the large-scale motions of proteins and their relation to protein function.

Quantitative analysis of molecularly stacked layer structures in supported organic thin films by synchrotron grazing-incidence X-ray scattering

Yoon, J. — 2007-04-21

In this study, we derive a grazing-incidence X-ray scattering (GIXS) formula to analyze quantitatively GIXS patterns for molecularly stacked layer structures in substrate-supported nanoscale thin films. We apply this formula in the quantitative analysis of GIXS patterns obtained for S-docosanylcysteine thin films on silicon substrates with native oxide layers. This analysis successfully provides information on the structural parameters and orientation of the molecular layer stack developed in S-docosanylcysteine thin films.

Micellar structure of amphiphilic poly(2-oxazoline) diblock copolymers

Papadakis, C.M. — 2007-04-21

Amphiphilic diblock copolymers from poly(2-oxazoline)s in aqueous solution can form micelles. By means of small-angle neutron scattering, we have found that poly[(n-nonyl-2-oxazoline)-b-(methyl-2-oxazoline)] {P[(NOx)-b-(MOx)]} diblock copolymers in aqueous solution form micelles of core-shell type. We have determined the core radius and the shell thickness of the micelles. Comparing the values obtained to the stretched lengths of the blocks leads to the conclusion that the P(NOx) core blocks are stretched, whereas the P(MOx) shell blocks are coiled.

Grazing-incidence small-angle X-ray scattering studies on templating nanopores in networked polymer thin films with a multi-armed porogen

Jin, K.S. — 2007-04-21

The mechanism of thermal pore generation in organosilicate thin films loaded with a six-armed star-shaped poly(ε-caprolactone) porogen was quantitatively investigated by using in-situ grazing-incidence small-angle X-ray scattering and thermogravimetry. These analyses found that the blend components have a limited miscibility that depends on the composition; for porogen loadings up to only 20 wt%, molecularly miscible blend films were obtained. Even for the miscible blend films, heating the films produced a curing reaction of the precursor matrix component, leading to the phase separation of the porogen component. This phase separation was found to begin at 393 K for 10 wt% porogen loaded films and at 373 K for 20 wt% porogen loaded films, and to continue for temperatures up to 423 K. The porogen aggregates remained and were confined within the matrix film without any further growth or movement until complete thermal decomposition above 564 K.

Pore lattice deformation in ordered mesoporous silica studied by in situ small-angle X-ray diffraction

Zickler, G.A. — 2007-04-21

Sorption and capillary condensation of an organic fluid in ordered mesoporous silica were studied by in situ small-angle X-ray diffraction using synchrotron radiation. The sorption isotherm was calculated from the sample transmission data. The diffraction peaks resulting from the periodic hexagonal arrangement of the pores show characteristic changes of intensity, position and width, and a pronounced hysteresis of these parameters in the capillary condensation/evaporation regime was observed. The change of the peak positions with gas pressure is related to pore lattice deformations due to capillary stresses occurring at the gas–liquid phase transition.

Complexity of silicate/aluminosilicate polymerization: some insights using a small-angle X-ray scattering study

Singh, P.S. — 2007-04-21

The small-angle X-ray scattering study reported here is on growth processes of particles that occurred during silicate/aluminosilicate polymerization starting from clear or colloidal solutions. Two polymerization reaction systems starting from clear homogeneous solutions of silicate monomers or oligomers, and two other polymerization reaction systems starting from silica colloidal solutions, were performed. Early growth of clearly defined silicate particles from a clear solution system was observed, whereas the scattering contrast of early growth processes from another clear system was close to that of the mother liquor and its weak scattering resulted from loosely aggregated structures. In the case of a colloidal solution system, the growth of silica particles was observed from the initial size of the silica nanoparticle reactant by reaction with aluminate anions on its surface, whereas in another colloidal system, depolymerization of the initial silica nanoparticle reactant into smaller silicate units and subsequently polymerization of the smaller silicate units with aluminate anions in solution was observed.

A quantitative analysis of small- and wide-angle X-ray diffraction curves of homogeneous ethylene-1-octene copolymers

Rabiej, S. — 2007-04-21

This paper presents a comparison of the results obtained with two methods employed in the analysis of small-angle X-ray scattering (SAXS) curves of isothermally crystallized homogeneous ethylene-1-octene copolymers: a method based on the calculation of the one-dimensional correlation function and a method based on model calculations and curve fitting. Data obtained from time-resolved SAXS investigations are supported by the results of simultaneous wide-angle X-ray diffraction (WAXD) measurements of crystallinity development during isothermal crystallization.

Structure of nickel nanoparticles in a microcrystalline cellulose matrix studied using anomalous small-angle X-ray scattering

Pirkkalainen, K. — 2007-04-21

Nickel nanoparticles were synthesized by adding aqueous nickel salt into a microcrystalline cellulose matrix. The NiII ions were reduced with either sodium borohydride, NaBH_4, or potassium hypophosphite, KH_2PO_2, in water or aqueous NH_3 medium. The mass fraction of Ni in the samples was between 3.7 and 8.9%. X-ray absorption spectra at the Ni K-edge showed that Ni was partially oxidized only in a sample reduced with NaBH_4. Wide-angle X-ray scattering results showed that nickel was in nanocrystalline or amorphous form in the samples. Upon heating fcc Ni, hcp Ni, NiO, Ni_3P and other Ni–P phases formed depending on the reduction parameters. Using anomalous small-angle X-ray scattering the nanometre-scale particle size distributions of the Ni particles were determined. A large fraction of particles less than 15 nm in size were observed in the samples reduced in aqueous ammonium compared with the samples reduced in water. Particles reduced in aqueous ammonium had a large ferromagnetic component.

Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg

Roessle, M.W. — 2007-04-21

The small-angle X-ray scattering beamline X33 of the European Molecular Biology Laboratory (EMBL) at the DORIS III storage ring [Deutsches Elektronen Synchrotron (DESY) Hamburg] was used for more than two decades to study the structure of non-crystalline biological systems. During recent years the beamline's scope has changed and is now predominantly used to analyze solutions of biological macromolecules. Owing to renewed interest in solution scattering studies from the biological community, the workload on the beamline has steadily increased. A major upgrade of X33 was performed to improve the beamline stability and data quality, to shorten the measurement time and to ensure user-friendly operation. The upgrade involved all major components of the beamline, including the optical system (monochromator, mirror, slits, beam monitors), electronics, control and acquisition software, X-ray detector system and the sample environment. The upgrade improved the brilliance by a factor of about three and the measuring time was reduced by a factor of seven. The knowledge and experience gained during the implementation of the upgrades to X33, may aid the design process for the BioSAXS beamline to be constructed for the PETRA-3 facility at DESY.

Mesoscopic structure in near-critical mixtures of D2O and 3-methylpyridine with salts

Sadakane, K. — 2007-04-21

Small-angle neutron scattering (SANS) experiments were performed on mixtures of 3-methylpyridine, D2O, and salts to investigate concentration fluctuations and structures in the vicinity of the critical point. The SANS profiles of ternary mixtures with large critical temperature shifts can be analyzed by the sum of the concentration fluctuation and a scattering from spherical clusters. The size of the clusters increases as the critical point is approached. These results can be interpreted in terms of a strong coupling of the critical fluctuation and the solvation effect of salt ions.

Contribution of synchrotron radiation to small-angle X-ray scattering studies in hard condensed matter

Simon, J.-P. — 2007-04-21

Synchrotron radiation, by virtue of its special beam characteristics (high flux, high brilliance, tuneable wavelength etc.), has revived interest in small-angle X-ray scattering (SAXS) for hard condensed matter and materials science. New techniques (ultra SAXS, grazing-incidence SAXS, X-ray photon correlation spectroscopy etc.) have been developed and new scientific themes tackled, ranging from metallurgy to nanotechnology.

The puzzle-interlayer model: an approach to the analysis of tightly packed arrangements of hard particles

Gille, W. — 2007-04-21

The small-angle scattering (SAS) structure functions are analyzed for an idealized, random two-phase system: a stationary arrangement of hard puzzle particles, separated by a relatively thin interspace, which can be approximated by an interlayer. The detailed shape of the interlayer is defined by the shape of the particles themselves: The starting point for producing these initial particles is a three-dimensional initial puzzle {P_0} in the state of tessellation. Its pieces, homogeneous particles of random shape, fit together filling the space. In a second step, an expanded puzzle {P_{\tau }} is constructed by translating the initial particles by a certain length \tau (relative to one another). The whole tightly packed particle arrangement depends on {P_0}. The interlayer region between the particles is a connected, homogeneous region. The SAS intensity of {P_{\tau }} depends on the parameter \tau and on the typical shape and size of the pieces of {P_0}. Chord length distributions (CLDs) are used in the description. The random shape of the pieces of {P_0} possesses a CLD 1. The CLD 2 of the intermediate spaces is approximated by that of an idealized layer of constant thickness \tau. The scattering of {P_{\tau}} results in terms of the CLDs of both phases. The approach can be applied to many types of {P_0}. Two initial tessellations of {P_0} are studied, a `dead leaves' tessellation produced by spherical primary grains and the Poisson plane mosaic.

Structural models of metastable phases occurring during the crystallization process of saturated/unsaturated triacylglycerols

Mykhaylyk, O.O. — 2007-04-21

Isothermal crystallizations of saturated and mixed saturated/unsaturated triacylglycerols (TAGs) have been studied by simultaneous time-resolved small-angle and wide-angle X-ray scattering measurements (SAXS/WAXS). The projection of the electron density profile along the layer normal derived from the lamellar peaks of the α2-phase can be assembled from two types of molecular dimers initially formed in the liquid state. One dimer corresponds to a typical two-chain packing of TAGs and the other is formed by opposing molecules overlapping by their two-acyl-chain sides. This structure occurs only in triacylglycerols containing both saturated and unsaturated acyl chains. The structural organization of the α2-phase is analogous to smectic A interdigitated phases. In the particular case of 1,3-distearoyl-2-oleoyl-sn-glycerol, StOSt, the α2-phase can evolve into a mixture of two phases (α1 and γ) with double and triple (2L and 3L) chain packing, respectively. A calculation of X-ray scattering patterns for simulated structures of randomly packed three-chain and two-chain layers of StOSt (2L + 3L) reproduced the three diffuse scattering peaks observed in the experimental SAXS patterns.

The new very-small-angle neutron scattering spectrometer at Laboratoire Léon Brillouin

Désert, S. — 2007-04-21

The design and characteristics of the new very-small-angle neutron scattering spectrometer under construction at the Laboratoire Léon Brillouin are described. Its goal is to extend the range of scattering-vector magnitudes towards 2 × 10−4 Å−1. The unique feature of this new spectrometer is a high-resolution two-dimensional image-plate detector sensitive to neutrons. The wavelength selection is achieved by a double-reflection supermirror monochromator and the collimator uses a novel multibeam design.

Discrepancy in determination of χ parameters by melting point depression versus small-angle neutron scattering in blends of deuterated polycarbonate and isotactic poly(methyl methacrylate)

Kyu, T. — 2007-04-21

The discrepancy in the χ interaction parameters of deuterated polycarbonate/isotactic poly(methyl methacrylate) blends as determined by the melting point depression approach and the small-angle scattering technique is reported. We have modified the Flory diluent theory by removing the inherent assumption of complete rejection of the solvent from the crystal solid by taking into consideration the crystal–amorphous, amorphous–crystal, and crystal–crystal interactions. The discrepancy in χ values obtained by the two methods is discussed.

Behaviour of materials in magnetic fields studied by small-angle X-ray scattering

Bras, W. — 2007-04-21

Traditionally the combination of electromagnetic fields and small-angle X-ray scattering has been mainly employed in the study of liquid crystals. However, with stronger magnetic fields becoming available owing to developments in superconductor technology it is possible to access a domain where larger macromolecular materials show, in some cases, a susceptibility to magnetic fields due to diamagnetic interactions. This effect can be used in several ways. The most obvious one is to use the alignment of the molecules to perform fibre diffraction experiments. Using an on-line split coil super-conducting magnet it is also possible to perform time-resolved studies on the re-orientation of, for instance, smectic liquid crystals under the influence of changing fields. In experiments where one is interested in the fundamental physics of liquid-crystal displays the use of magnetic fields often is preferred over the use of electric fields since there are fewer problems with ionic sample contaminations and temperature dependent susceptibilities.

Small-angle X-ray study of the three-dimensional collagen/mineral superstructure in intramuscular fish bone

Zhou, H. — 2007-04-21

Synchrotron small-angle X-ray scattering (SAXS) was conducted on native intramuscular shad/herring bone samples. Two-dimensional SAXS patterns were quantitatively analyzed with special consideration for preferred orientation effects, leading to new insights into the three-dimensional superstructure of mineralized collagen fibrils in shad/herring bone.

Complementary use of small-angle neutron scattering and dynamic light scattering studies for structure analysis and dynamics of polymer gels

Shibayama, M. — 2007-04-21

Small-angle neutron scattering (SANS) and dynamic light scattering (DLS) have been complementarily employed in order to investigate the structure and dynamics of slide-ring (SR) gels, a class of novel polymer gels having advanced mechanical properties. SR gels consist of long flexible polymer chains and movable cross-links along the polymer chain. It is demonstrated that complementary use is necessary to explore the dynamics of SR gels. The sliding capability was verified by DLS and a low level of frozen inhomogeneities, originating from the sliding motion, was observed by SANS. DLS was also used to determine the sol–gel transition threshold and to decompose the scattering intensity into the dynamic fluctuating component and the frozen inhomogeneities. Both techniques clearly indicate the presence of the sliding mode in SR gels, which plays significant roles in the advanced mechanical and swelling properties.

Fracture of poly(vinylidene fluoride): a combined synchrotron and laboratory in-situ X-ray scattering study

Maier, G.A. — 2007-04-21

Semi-crystalline polymers show a complex fracture mechanism, which is controlled by the micro-mechanisms associated with formation and breakdown of a plastic deformation region. Such regions develop at notches, cracks or other stress-raising defects. In the present paper, we use time-resolved synchrotron X-ray scattering techniques during the deformation process in poly(vinylidene fluoride) to study the plastic zone formation and fracture processes at different strain rates. This gives new insight into the micro-mechanisms of cavitation, lamellae separation and fibril formation in this particular material.

Synchrotron X-ray scattering and reflectivity studies of the structure of low dielectric constant SiOCH thin films prepared from bistrimethylsilylmethane by chemical vapor deposition

Heo, K. — 2007-04-21

Quantitative, non-destructive grazing-incidence X-ray scattering and specular X-ray reflectivity analysis with synchrotron radiation sources, along with spectroscopic ellipsometry analysis, were successfully used to characterize a series of low dielectric constant, nanoporous SiOCH dielectric thin films with nanometre-scale thicknesses prepared by radio-frequency inductively coupled plasma chemical vapor deposition of bistrimethylsilylmethane precursor and oxygen gas at various flow rate ratios followed by annealing at 298, 473, 573 or 673 K. These analyses provided important information on the structures and properties of the nanoporous films. The average size of the nanopores generated in each film was 3.07 nm in radius or less, depending on the process conditions. The film electron densities ranged from 414 to 569 nm−3, the refractive indices ranged from 1.434 to 1.512 at 633 nm wavelength, and the porosities ranged from 16.1 to 38.9%. Collectively, the present findings show that SiOCH thin films of the type reported here are suitable for use as low dielectric constant interdielectric layer materials in the fabrication of advanced integrated circuits.

Hierarchical structures formed by partially crystalline polymers in solution: from fundamentals to applications – a combined conventional, focusing and ultra-small-angle neutron scattering study

Radulescu, A. — 2007-04-21

Multilevel aggregates with characteristic sizes covering four orders of magnitude, from 1 nm to 10 µm, are formed upon cooling decane solutions of poly(ethylene-butene) random copolymers (designated as PEB-n, where n is the number of ethyl side branches per 100 backbone C atoms) and wax-containing mixed solutions. The partially crystalline PEB-7.5 copolymers form two distinct morphologies that evolve on a range of length scales. When these polymers are mixed with wax molecules having a crystallization point lower than the polymer aggregation temperature, a hierarchy of morphologies evolves on decreasing the temperature. The multilevel structures were elucidated by combining conventional small-angle neutron scattering, focusing small-angle neutron scattering and ultra-small-angle neutron scattering investigations with microscopy. Contrast-matching analysis of the wax and copolymer components within the common morphologies revealed the wax-crystal modification capacity of the PEB-7.5 copolymers. Since the copolymers limit the growth of wax crystals, they are potential pour-point depressants for the fuel industry.

Time domain effects in the single-chain dynamics of semidilute and concentrated polymer solutions

Tchesskaya, T.Y. — 2007-04-21

Single-chain dynamics in semidilute polymer solutions is Zimm-like on short time scales and Rouse-like on long time scales. The crossover is due to time-dependent screening of hydrodynamic interactions. We present a generalized Zimm theory for polymer dynamics in an elastic polymer network. We show that the coupled equations of motion of the polymer network–fluid system lead to a generalized Oseen tensor with a time-dependent hydrodynamic screening length. The time correlation function of the Rouse modes, monomer mean-square displacements and the single-chain dynamical structure factor are calculated.

Grazing-incidence small-angle X-ray scattering study of porous dielectrics used in advanced microelectronic interconnections

Simon, J.-P. — 2007-04-21

The increase of the integration density and of the operation speed in ultra-large-scale integrated microelectronics requires a reduction in the dielectric constant for high-frequency insulation between the copper connections of some tenth-of-micrometre thickness. Recently, the quality of the dielectric has been defined by its dielectric constant k (>1) relative to the unpolarized vacuum (k = 1). Bulk low k will never reach k lower than 3 and the only way to achieve a further decrease in k is to introduce nanoporous dielectric films compatible with the required mechanical behaviour. We compare the merits and the structure determined by grazing-incidence small-angle X-ray scattering (GISAXS) of four different growth processes: plasma-enhanced chemical vapour deposition or spin coating with three variants: dual-phase blend, self-assembled approach, nanoclustering precursor. All of them are baked in order to cure the amorphous SiwOxCyHz `skeleton' (SiOCH). Depending on the process used, the pore morphologies are very different. They range from well defined pores of 4–5 nm diameter to sub-nanometric ill-defined pores which may be described as density fluctuations. Finally, it appears that the curing process is a key problem, which up to now has been difficult to characterize by GISAXS.

Small-angle X-ray scattering from polystyrene polymacromonomers with relatively short main chains

Nakamura, Y. — 2007-04-21

Synchrotron small-angle X-ray scattering measurements were made on polystyrene polymacromonomers F33 and F110 with 33 and 110 styrene residues, respectively, in each side chain in toluene at 298.2 K and cyclohexane at 307.7 K. Two F33 samples with different weight-average degrees of polymerization of main chain Nw of 37 and 17 (F33-13 and F33-14, respectively) and two F110 samples with Nw of 61 and 27 (F110-10 and F110-11, respectively) were used. The z-average mean-square radii of gyration of these polymacromonomers were explained by the wormlike chain with finite diameter when we considered the contribution of side chains near the main chain to the contour length. This model was also applied to calculate the particle scattering function P(θ), giving satisfactory agreements between calculated and experimental k2P(θ) for F33-13 and F110-10 plotted against the magnitude of the scattering vector k = (4π/λ0)sin(θ/2), where λ0 and θ denote the wavelength of the incident X-ray and the scattering angle, respectively. The data for F33-14 and F110-11, which have short main chains relative to the side chains, cannot be explained by the same model. However, these data were closely fitted by the theoretical values for a comb polymer model with semiflexible main and side chains. The stiffness parameter for side chains in toluene was larger than that in cyclohexane, suggesting that the side chains in the former solvent are more stretched than those in cyclohexane.

Structural analysis of thin films of novel polynorbornene derivatives by grazing incidence X-ray scattering and specular X-ray reflectivity along with ellipsometry

Lee, T.J. — 2007-04-21

In the present study, structural analyses using synchrotron grazing incidence X-ray scattering, specular reflectivity and ellipsometry were performed on thin films of two novel polynorbornene derivatives, chiral poly(norbornene acid methyl ester) and racemic poly(norbornene acid n-butyl ester), which are potential low dielectric constant materials for advanced microelectronic and display applications. These analyses provided important information on the structure, electron density gradient across the film thickness, chain orientation, refractive index and thermal expansion characteristics of the polymers in substrate-supported thin films. The structural characteristics and properties of the thin films depended on the tacticity of the polymer chain and were further influenced by the film thickness and thermal annealing history.

Creating local contrast in small-angle neutron scattering by dynamic nuclear polarization

van den Brandt, B. — 2007-04-21

Low-resolution small-angle neutron scattering measurements can benefit from polarized protons to generate scattering contrast profiles. In a recently developed technique, time-resolved polarized SANS tries to make use of spatial polarization gradients created around paramagnetic centres at the onset of dynamic nuclear polarization. The time constants which describe the build-up of polarization around the paramagnetic centre and the subsequent diffusion of polarization in the solvent were determined by analysing the temporal evolution of the nuclear polarization. The possible use and the limitations of this technique as a spectroscopic tool are discussed.

Hierarchical bionanotubes formed by the self assembly of microtubules with cationic membranes or polypeptides

Raviv, U. — 2007-04-21

At present there is a surge in interest in biophysical research aimed at elucidating collective interactions between cellular proteins and associated biomolecules leading to supramolecular structures, with the ultimate goal of relating structure to function. The nerve cell cytoskeleton provides a rich example of highly ordered bundles and networks of interacting neurofilaments, microtubules and filamentous actin, where the nature of the interactions, structures and structure–function correlations remain poorly understood. We present synchrotron X-ray diffraction and electron microscopy data, in reconstituted protein systems from the bovine central nervous system, which reveal unexpected structures not predicted by current electrostatic theories. By mixing preassembled microtubules with charged membranes or polypeptides we found hierarchical bionanotubes made of microtubules coated by lipid bilayers or polypeptides, which in turn are coated with a third layer of tubulin oligomers forming rings or spirals.

Thermal radiation method: proposal of a new technique for measuring interfacial or surface fluctuations

Kajihara, Y. — 2007-04-21

A thermal radiation method is proposed as a new technique for measuring interfacial or surface fluctuations. From Kirchhoff's law, the intensity includes diffuse scattering, which means that it can be used to measure mesoscopic fluctuations of samples like a small-angle X-ray or neutron scattering method. We applied the method to mercury on a sapphire system where the mercury wets the sapphire by a first-order phase transition (prewetting) at high temperature and high pressure, and thus large fluctuations in the film can be expected in its supercritical region. We succeeded in measuring huge surface fluctuations in the film.

The new V12 ultra-small-angle neutron scattering and tomography instrument at the Hahn–Meitner Institut

Strobl, M. — 2007-04-21

The new V12 instrument at the Hahn–Meitner Institute in Berlin is a multiple setup combining several techniques to investigate the internal structure of bulk samples. It consists of two double-crystal diffractometers (DCDs) and an attenuation tomography device operating with monochromatic neutrons. The three instrument parts can be used independently at the same time. The DCDs are mainly used in the ultra-small-angle neutron scattering (USANS) regime, where they overlap the accessible range of small-angle neutron scattering instruments, while tomographic methods collect real-space information on a macroscopic scale. Together they enable structural investigations over six orders of magnitude (50 nm to 5 cm). Scattering and tomographic methods can even be combined by means of diffraction and scattering-enhanced imaging. The sample environment can be varied over a large range of temperatures and pressures for USANS measurements and a polarized USANS option is available.

Current status of the 40 m small-angle neutron scattering instrument development at the HANARO research reactor

Han, Y.-S. — 2007-04-21

The cold neutron research facility project at the Korean HANARO research reactor was launched in 2003. A state-of-the-art small-angle neutron scattering instrument was selected as a top-priority instrument. An analytical calculation was used to obtain the optimum instrument design and the appropriate range of scattering vectors of the instrument. Then, in order to optimize the instrument layout and to enhance the instrument's performance, a Monte Carlo simulation was performed. The Q range [where Q is the magnitude of the scattering vector given by (4π/λ)sin(θ/2), θ is the scattering angle and λ is the wavelength] of the instrument will extend from 0.0008 to 1.0 Å−1. The instrument layout was optimized based on simulation results. The maximum flux at the sample position can reach about 5.5 × 10 7 n cm−2 s−1.

Probing the flow-induced shish-kebab structure in entangled polyethylene melts by synchrotron X-ray scattering

Keum, J.K. — 2007-04-21

In-situ rheo small-angle X-ray scattering (SAXS) and rheo wide-angle X-ray diffraction (WAXD) techniques were used to investigate the flow-induced crystalline structure in entangled melts of ultrahigh-molecular-weight polyethylene (UHMWPE)/low-molecular-weight polyethylene (LMWPE) blends (0, 2 and 5 wt% of UHMWPE). Immediately after a step shear at 415 K, SAXS and WAXD results confirmed that only the shish structure was formed in the melts without kebabs. The topological deformation of entangled UHMWPE chains in the blend was responsible for the formation of shish. The missing kebab growth in the presence of shish indicated that secondary nucleation of coiled chains on the shish surface was frustrated at high temperatures close to the equilibrium melting temperature (418.5 K). When the temperature was quenched to 407 K, both blends (but not pure LMWPE) clearly exhibited oriented kebab growth. An Avrami analysis was applied to investigate the nucleation and growth of kebabs. Results indicated that kebabs were probably grown under athermal nucleation and diffusion-controlled conditions. In addition, the crystallization rate under predetermined nucleation was strongly governed by the concentration of shish.

The CCP13 FibreFix program suite: semi-automated analysis of diffraction patterns from non-crystalline materials

Rajkumar, G. — 2007-02-01

The extraction of useful information from recorded diffraction patterns from non-crystalline materials is non-trivial and is not a well defined operation. Unlike protein crystallography where one expects to see well behaved diffraction spots in predictable positions defined by standard space groups, the diffraction patterns from non-crystalline materials are very diverse. They can range from uniaxially oriented fibre patterns which are completely sampled as Bragg peaks, but rotationally averaged around the fibre axis, to fibre patterns that are completely unsampled, to either kind of pattern with considerable axial misalignment (disorientation), to liquid-like order and even to mixtures of these various structure types. In the case of protein crystallography, the specimen is generated artificially and only used if the degree of order is sufficient to yield a three-dimensional density map of high enough resolution to be interpreted sensibly. However, with non-crystalline diffraction, many of the specimens of interest are naturally occurring (e.g. cellulose, rubber, collagen, muscle, hair, silk) and to elucidate their structure it is necessary to extract structural information from the materials as they actually are and to whatever resolution is available. Even when synthetic fibres are generated from purified components (e.g. nylon, polyethylene, DNA, polysaccharides, amyloids etc.) and diffraction occurs to high resolution, it is rarely possible to obtain perfect uniaxial alignment. The CCP13 project was established in the 1990s to generate software which will be generally useful for analysis of non-crystalline diffraction patterns. Various individual programs were written which allowed separate steps in the analysis procedure to be carried out. Many of these programs have now been integrated into a single user-friendly package known as FibreFix, which is freely downloadable from http://www.ccp13.ac.uk. Here the main features of FibreFix are outlined and some of its applications are illustrated.

Structure of nanoporous zirconia-based powders synthesized by different gel-combustion routes

Casanova, J.R. — 2007-04-21

Zirconia-based ceramics that retain their metastable tetragonal phase at room temperature are widely studied due to their excellent mechanical and electrical properties. When these materials are prepared from precursor nanopowders with high specific surface areas, this phase is retained in dense ceramic bodies. In this work, we present a morphological study of nanocrystalline ZrO2–2.8 mol% Y2O3 powders synthesized by the gel-combustion method, using different organic fuels – alanine, glycine, lysine and citric acid – and calcined at temperatures ranging from 873 to 1173 K. The nanopore structures were investigated by small-angle X-ray scattering. The experimental results indicate that nanopores in samples prepared with alanine, glycine and lysine have an essentially single-mode volume distribution for calcination temperatures up to 1073 K, while those calcined at 1173 K exhibit a more complex and wider volume distribution. The volume-weighted average of the nanopore radii monotonically increases with increasing calcination temperature. The samples prepared with citric acid exhibit a size distribution much wider than the others. The Brunauer–Emmett–Teller technique was used to determine specific surface area and X-ray diffraction, environmental scanning electron microscopy and transmission electron microscopy were also employed for a complete characterization of the samples.

Gibbs–Thomson analysis of crystalline poly(9,9-di-n-octyl-2,7-fluorene)

Chen, S.H. — 2007-04-21

Based on results of small-angle X-ray scattering and differential scanning calorimetric measurements, the equilibrium melting temperature and basal surface energy (σe) of crystalline poly(9,9-di-n-octyl-2,7-fluorene) (PFO) were preliminarily estimated as ca 451.6 K and 0.084 J m−2, respectively, via Gibbs–Thomson analysis. This σe value leads to a value of 76 kJ mol−1 for the work of fold that greatly exceeds the values for typical polymers, reflecting the semi-rigid nature of the PFO backbone and consistent with the large-loop folds proposed earlier for this particular conjugated-backbone polymer. This is in strong contrast to the commonly held belief that conjugated polymers are generally too rigid to form folded-chain lamellar crystals.

Large-scale and local-scale structures in polymer-blend films: a grazing-incidence ultra-small-angle X-ray scattering and sub-microbeam grazing-incidence small-angle X-ray scattering investigation

Müller-Buschbaum, P. — 2007-04-21

Phase-separation structures are installed by solution casting and flow of a binary polymer-blend solution of polystyrene and poly-n-butylacrylate in toluene on silicon. Optical microscopy and scanning-probe microscopy measurements provide the surface topography. Large-scale structures are probed with high-resolution or grazing-incidence ultra-small-angle X-ray scattering enabled by high reciprocal-space resolution. Correspondingly, structures of up to 13 µm are resolved. Local-scale structures are detected with sub-microbeam grazing-incidence small-angle X-ray scattering, providing a high real-space resolution of 1 µm. Nanometre-size cavities are found in the polystyrene-rich parts of the blend film.

Hydrostatic low-range pressure applications of the Paris–Edinburgh cell utilizing polymer gaskets for diffuse X-ray scattering measurements

Chapman, K.W. — 2007-02-01

The use of a polymeric Torlon (polyamide–imide) gasket material in a Paris–Edinburgh pressure cell for in situ high-pressure X-ray scattering measurements is demonstrated. The relatively low bulk modulus of the gasket allows for fine control of the sample pressure over the range 0.01–0.42 GPa. The quality of the data obtained in this way is suitable for Bragg and pair distribution function analysis.

Investigation of symmetry-breaking flux-line lattice phases in superconductors by small-angle neutron scattering

Forgan, E. — 2007-04-21

In single-crystal superconductors in the mixed state, flux-line structures may have a lower symmetry than the host crystal. In this case, multiple degenerate flux lattice domains may be present simultaneously and give rise to complicated small-angle diffraction patterns. The interpretation of these patterns in terms of the flux lattice structure in a single domain is discussed, with particular reference to recently reported spontaneous symmetry-breaking flux-line lattice phases in niobium.

Field-dependent relaxation behavior of Co-ferrofluid investigated with stroboscopic time-resolved small-angle neutron scattering

Keiderling, U. — 2007-04-21

In an external magnetic field, concentrated Co-ferrofluids form an inter-particle order revealing coexistence of a pseudo-crystalline hexagonal ordering of core-shell nanoparticles and segments of dipolar chains. The decay of this order after switching off the magnetic field is characterized by time constants of a few seconds. This relaxation behaviour has been investigated using a newly developed stroboscopic small-angle neutron scattering technique based on listmode data acquisition. This technique utilizes the fact that the process of creation and decay of the inter-particle order is reversible, thus allowing very good scattering statistics to be gained by stroboscopically repeating the process and superimposing the data from the individual cycles. This paper presents time constants determined for the decay of inter-particle order states created by different external magnetic fields. The decay is generally characterized by an exponential course, assigned to Brownian rotation of locally ordered domains, although in the very beginning it appears to take place faster, indicating a different decay mechanism. The time constants at fields > 0.1 T significantly increase, indicating a larger size of the ordered domains resulting from enhanced dipolar interactions.

Synchrotron X-ray reflectivity studies of nanoporous organosilicate thin films with low dielectric constants

Oh, W. — 2007-04-21

Quantitative, non-destructive X-ray reflectivity analysis using synchrotron radiation sources was successfully performed on nanoporous dielectric thin films prepared by thermal processing of blend films of a thermally curable polymethylsilsesquioxane dielectric precursor and a thermally labile triethoxysilyl-terminated six-arm poly(∊-caprolactone) porogen in various compositions. In addition, thermogravimetric analysis and transmission electron microscopy analysis were carried out. These measurements provided important structural information about the nanoporous films. The thermal process used in this study was found to cause the porogen molecules to undergo efficiently sacrificial thermal degradation, generating closed, spherical nanopores in the dielectric film. The resultant nanoporous films exhibited a homogeneous, well defined structure with a thin skin layer and low surface roughness. In particular, no skin layer was formed in the porous film imprinted using a porogen loading of 30 wt%. The film porosities ranged from 0 to 33.8% over the porogen loading range of 0–30 wt%.

Iron K-edge anomalous small-angle X-ray scattering at 15-ID-D at the Advanced Photon Source

Kirby, N. — 2007-04-21

Small-angle X-ray scattering (SAXS) is an ideal technique for characterizing inorganic nanoparticles in biological specimens large enough to be representative of tissues. As tissues consist of complex mixtures of structures, identifying particular structural features from single-wavelength scattering data can be problematic. Synchrotron SAXS can supply element-specific structural information in complex samples, using anomalous scattering close to absorption edges. Anomalous dispersion is a secondary effect that produces relatively subtle changes in scattering patterns. In order to utilize this effect for anomalous SAXS analysis, stringent control of instrument performance is required. This work outlines the development of high-quality data collection and processing strategies for Fe K-edge anomalous SAXS on the ChemMatCARS beamline at the Advanced Photon Source (APS), Chicago, with an emphasis on intensity normalization. The methods reported here were developed during a study of iron-loaded mammal tissues, but could equally well be applied to other complex specimens.

Development of an ultra-small-angle X-ray scattering instrument for probing the microstructure and the dynamics of soft matter

Sztucki, M. — 2007-04-21

A Bonse–Hart camera suitable for studying dilute and weakly scattering systems has been developed. The required level of reduction of the parasitic background scattering was realised by replacing channel-cut crystals by a pair of polished and deeply etched parallel crystals. The performance of this ultra-small-angle X-ray scattering instrument is illustrated by means of two examples: the microstructure of a short-range attractive colloidal system; and the growth dynamics of soot particles in a diffusion flame. In addition, the feasibility of performing dynamic X-ray scattering experiments is demonstrated.

Permeability of water through a raft model membrane clarified by time-resolved SANS and SAXS

Hirai, M. — 2007-04-21

We have characterized the structures of ganglioside (GD3) micelle and GD3/cholesterol mixtures, and have determined the permeability of water across a membrane of GD3/cholesterol/phospholipid uni-lamellar vesicle. We have found that monovalent Na+ and K+ cations affect the permeability of water differently. We have found also that the permeability of water is greatly enhanced by the K+ ion, suggesting the function of the GD3/cholesterol rich clusters on neuronal excitations by K+. The complimentary use of small-angle X-ray and neutron scattering techniques is useful to determine the permeability of water across a vesicle membrane.

A new experimental station for simultaneous X-ray microbeam scanning for small- and wide-angle scattering and fluorescence at BESSY II

Paris, O. — 2007-04-21

A new instrument for simultaneous microbeam small- and wide-angle X-ray scattering and X-ray fluorescence (SAXS/WAXS/XRF) is presented. The instrument is installed at the microfocus beamline at BESSY II and provides a beam of 10 µm size with a flux of about 109 photons s−1. A SAXS resolution up to 500 Å d-spacing and a range of scattering vectors of almost three orders of magnitude are reached by using a large-area high-resolution CCD-based detector for simultaneous SAXS/WAXS. The instrument is particularly suited for scanning SAXS/WAXS/XRF experiments on hierarchically structured biological tissues. The necessary infrastructure, such as a cryo-stream facility and an on-site preparation laboratory for biological specimens, are available.

CMOS flatpanel detectors for SAXS/WAXS experiments

Yagi, N. — 2007-04-21

A CMOS (complementary metal-oxide semiconductor) flatpanel X-ray detector is a two-dimensional silicon image sensor with a scintillator. We have tested the performance of two types of CMOS detectors in simultaneous small-angle/wide-angle X-ray scattering experiments. Both are active-pixel devices that have an amplifier in each pixel. Wide-angle patterns were recorded with the detector just behind the specimen and very close to the beam. The quality of the images shows that these detectors are suitable for this purpose.

GISAXS study of cavities and {113} defects induced by neon and helium implantation in silicon

Babonneau, D. — 2007-04-21

Grazing incidence small-angle X-ray scattering experiments have been performed to study the morphology of nanocavities and {113} defects formed by implantation of 5 \times 10^{16} cm^{-2} neon and helium ions in Si(001) at 50 keV. The results show that spherical cavities are formed in Si(001) implanted with Ne ions at 873 K and in Si(001) implanted with He ions at 473 K subsequently annealed at 873 K. In contrast, He-induced cavities at 873 K show {111} facets and wide size distribution due to an enhanced He mobility at high temperature. In addition to the faceted cavities, the clustering of interstitials leads to the formation of large extended planar {113} defects whose size has been estimated to be about 100 nm.

Crystal structure prediction of organic pigments: quinacridone as an example

Panina, N. — 2007-02-01

The structures of the α, β and γ polymorphs of quinacridone (Pigment Violet 19) were predicted using Polymorph Predictor software in combination with X-ray powder diffraction patterns of limited quality. After generation and energy minimization of the possible structures, their powder patterns were compared with the experimental ones. On this basis, candidate structures for the polymorphs were chosen from the list of all structures. Rietveld refinement was used to validate the choice of structures. The predicted structure of the γ polymorph is in accordance with the experimental structure published previously. Three possible structures for the β polymorph are proposed on the basis of X-ray powder patterns comparison. It is shown that the α structure in the Cambridge Structural Database is likely to be in error, and a new α structure is proposed. The present work demonstrates a method to obtain crystal structures of industrially important pigments when only a low-quality X-ray powder diffraction pattern is available.

Parametric Rietveld refinement

Stinton, G.W. — 2007-02-01

In this paper the method of parametric Rietveld refinement is described, in which an ensemble of diffraction data collected as a function of time, temperature, pressure or any other variable are fitted to a single evolving structural model. Parametric refinement offers a number of potential benefits over independent or sequential analysis. It can lead to higher precision of refined parameters, offers the possibility of applying physically realistic models during data analysis, allows the refinement of `non-crystallographic' quantities such as temperature or rate constants directly from diffraction data, and can help avoid false minima.

ENGIN-X: a third-generation neutron strain scanner

Santisteban, J.R. — 2006-12-01

ENGIN-X, a new time-of-flight (TOF) neutron diffractometer optimized to measure elastic strains at precise locations in bulky specimens recently commissioned at the ISIS Facility in the Rutherford Laboratory, UK, is described. Fast counting times, together with a flexible and accurate definition of the instrumental gauge volume are the main requirements of neutron strain scanning and have been addressed on ENGIN-X through the design of a novel TOF diffractometer with a tuneable resolution and interchangeable radial collimators. Further, the routine operation of the instrument has been optimized by creating a virtual instrument, i.e. a three-dimensional computer representation of the diffractometer and samples, which assists in the planning and execution of experiments. On comparing ENGIN-X with its predecessor ENGIN, a 25× gain in performance is found, which has allowed the determination of stresses up to 60 mm deep in steel specimens. For comparison with constant-wavelength diffractometers, special attention has been paid to the absolute number of counts recorded during the experiments. A simple expression is presented for the estimation of counting times in TOF neutron strain scanning experiments.

An automated platform for parallel crystallization of small organic molecules

Florence, A.J. — 2006-12-01

An automated platform for parallel crystallization of small organic molecules from solution is described. The principal gain over manual crystallization lies in the automated sequencing of crystallization steps, including computer-controlled dosing of liquids and solids. The platform is designed to conduct 32 crystallizations per day, from solution volumes up to 10 ml, allowing a search for physical forms to be conducted over a finer grid than might be accessible manually and thereby increasing the probability of success.

Three-dimensional birefringence imaging with a microscope tilting stage. II. Biaxial crystals

Pajdzik, L.A. — 2006-12-01

The technique enables precise three-dimensional birefringence information of optically biaxial materials to be obtained. Equations derived here describe a mathematical model of the tilting-stage system for such crystals in any general orientation. This leads to precise values of the three principal birefringences and the optical orientation. The method is also able to obtain information on preferred orientation in a biaxial polycrystalline material, providing comprehensive information on both optical orientation of crystallites and spatial resolution. In addition, an unknown crystalline material may be identified, or at least classified within a specific group of crystalline materials.

Structure matching: measures of similarity and pseudosymmetry

Collins, A. — 2006-12-01

A sizeable proportion of structures with Z′ = 2 are thought to exhibit pseudosymmetry, but establishing the extent of the deviation from true symmetry is problematic. By considering both the conformational similarity between the independent molecules and the way in which they are related in space, assessment of the pseudosymmetry of a structure becomes possible. A method of matching two groups of atoms where both these factors are quantified using CRYSTALS [Betteridge, Carruthers, Cooper, Prout & Watkin (2003). J. Appl. Cryst. 36, 1487] is described.

Thin film analysis by X-ray scattering. By Mario Birkholz, with contributions by P. F. Fewster and C. Genzel. Pp. xxii+356. Weinheim: Wiley-VCH Verlag GmbH Co., 2005. Price (hardcover) EUR 119, SFR 188. ISBN-10: 3-527-31052-5; ISBN-13: 978-3-527-31052-4.

Chateigner, D. — 2006-12-01

Optical anomalies in crystals. By A. G. Štukenberg and Ju. O. Punin. (In Russian.) Pp. 263. St. Petersburg: Izdanya Nauka, 2004. Price (hardback) USD 26.95.

Paufler, P.P. — 2006-10-01

SXD – the single-crystal diffractometer at the ISIS spallation neutron source

Keen, D.A. — 2006-10-01

SXD, the single-crystal diffractometer at the ISIS spallation neutron source, uses an array of two-dimensional position-sensitive detectors and the neutron time-of-flight technique to measure diffraction data throughout very large volumes of reciprocal space for each fixed orientation of a single-crystal sample. This paper describes SXD in detail, following major improvements to the instrument. Particular emphasis is placed on the range of science possible, using recent results as examples, and the opportunities for future experiments.

Stephen Fleet

Cooper, M. — 2006-08-01

In situ SAXS studies of the morphological changes of an alumina–zirconia–silicate ceramic during its formation

Le Messurier, D. — 2006-08-01

Small-angle X-ray scattering is used at two energies, one either side of the zirconium K-edge, to probe the in situ formation of an alumina–zirconia–silicate ceramic. The use of energies either side of the edge allows the decomposition of information regarding the scattering from the zirconia particles from that of the glass matrix. Porod slope data show how the nanoparticles progress from being relatively isolated particles to becoming agglomerates as the pore network in the glass collapses. The shape of the agglomerates resembles the pore network of the glass at low temperature. The Guinier radii of the particles show the growth of the agglomerates past the Littleton softening point, whilst still resolving the primary particles.

Crystallography on mobile phones

Orlov, I. — 2006-08-01

The new possibilities offered by mobile phones combined with their widespread dissemination among young people open new paradigms for teaching science. The wide adoption of the Java environment for mobile devices gives the opportunity to develop custom-made applications for educational purposes. The first mobile phone application for crystallography training, Escher Mobile, is now available at http://escher.epfl.ch/mobile/.

Protein crystallography with a novel large-area pixel detector

Hülsen, G. — 2006-08-01

The PILATUS 1M detector, developed at the Paul Scherrer Institut, is a single-photon-counting hybrid pixel detector designed for macromolecular crystallography. With more than 1 million pixels covering an area of 243 × 210 mm, it is the largest such device constructed to date. The detector features a narrow point spread function, very fast readout and a complete absence of electronic noise. Unfortunately, this prototype detector has numerous defective pixels and sporadic errors in counting that complicate its operation. With appropriate experimental design, it was largely possible to work around these problems and successfully demonstrate the application of this technology to structure determination. Conventional coarse φ-sliced data were collected on thaumatin and a refined electron density map was produced that showed the features expected of a map at 1.6 Å resolution. The results were compared with the performance of a reference charge-coupled device detector: the pixel detector is superior in speed, but showed higher R-factors because of the counting errors. Complete fine φ-sliced data sets recorded in the continuous-rotation mode showed the predicted advantages of this data collection strategy and demonstrated the expected reduction of R-factors at high resolution. A new readout chip has been tested and shown to be free from the defects of its predecessor; a PILATUS 6M detector incorporating this new technology is under construction.

A validating CIF parser: PyCIFRW

Hester, J.R. — 2006-08-01

PyCIFRW is a general-purpose Python package providing a simple, powerful interface for working with CIF files. Objects and methods are available for reading, writing and manipulating CIF files and dictionaries. Comprehensive validation of CIF files and dictionaries against DDL1 or DDL2 dictionaries is also possible. PyCIFRW is easily included in larger projects and is portable across a large number of platforms. Although written in an interpreted language, parsing and validation times are acceptable for most applications.

A deconvolution method for the reconstruction of underlying profiles measured using large sampling volumes

Xiong, Y.-S. — 2006-06-01

A deconvolution method for diffraction measurements based on a statistical learning technique is presented. The radial-basis function network is used to model the underlying function. A full probabilistic description of the measurement is introduced, incorporating a Bayesian algorithm based on an evidence framework. This method allows predictions of both the convolution and the underlying function from noisy measurements. In addition, the method can provide an estimation of the prediction uncertainty, i.e. error-bars. In order to assess the capability of the method, the model was tested first on synthetic data of controllable quality and sparsity; it is shown that the method works very well, even for inaccurately measured (noisy) data. Subsequently, the deconvolution method was applied to real data sets typical of neutron and synchrotron residual stress (strain) data, recovering features not immediately evident in the large-gauge-volume measurements themselves. Finally, the extent to which short-period components are lost as a function of the measurement gauge dimensions is discussed. The results seem to indicate that for a triangular sensor-sensitivity function, measurements are best made with a gauge of a width approximately equal to the wavelength of the expected strain variation, but with a significant level of overlap (∼80%) between successive points; this is contrary to current practice for neutron strain measurements.

Si wafers having one- and two-dimensionally curved (111) planes examined by X-ray diffraction

Okuda, H. — 2006-06-01

Si (111) wafers deformed at elevated temperatures into cylindrical or hemispherical shapes have been examined by X-ray diffraction. Well defined 333 peaks shifted with in-plane distance from the centre of the wafer as determined by ω scans. The shift of the peak position agreed with the curvature of the Si wafer, suggesting that the Si (111) lattice plane can be designed on an arbitrarily curved surface by this method. These crystals have potential for innovative applications in X-ray instrumentation, for both diffraction/scattering and spectroscopy.

Characterization of insulin microcrystals using powder diffraction and multivariate data analysis

Norrman, M. — 2006-06-01

Twelve different microcrystalline insulin formulations were investigated by X-ray powder diffraction and were shown to have very characteristic patterns. Three of the formulations crystallize in the same crystal system, but have structural differences in the N-terminal B-chain of the insulin molecule. This difference was efficiently detected in the powder patterns. The sensitivity of the method makes it a valuable tool for characterization of microcrystalline samples. By use of principal-component analysis, the twelve different formulations originating from six different crystal systems were classified into nine separate clusters. The powder patterns of each cluster can now be used as `fingerprints' for the different insulin polymorphs. The combination of X-ray powder diffraction and multivariate analysis, such as principal-component analysis, provides a rapid and effective tool for studying the influence of derivatives, additives, ions, pH etc., in the crystallization media.

A Crystallographic Information File for specular reflectivity data

van der Lee, A. — 2006-06-01

The instrumental resolution function of synchrotron radiation powder diffractometers in the presence of focusing optics

Gozzo, F. — 2006-06-01

The theory developed by Caglioti and co-workers [Caglioti, Paoletti & Ricci (1958). Nucl. Instrum. 3, 223–228; Caglioti, Paoletti & Ricci (1960). Nucl. Instrum. Methods, 9, 195–198; Caglioti & Ricci (1962). Nucl. Instrum. Methods, 15, 155–163] and Sabine [(1987). J. Appl. Cryst. 20, 23–27, 173–178] that provides an analytical description of the instrumental resolution function of single-crystal and powder diffractometers consisting of sequences of collimators and crystals is extended by including the effect of collimating and refocusing mirrors. A simple analytical expression with only two fitting parameters (the beam divergence after reflection by the collimating and the refocusing mirrors) is determined, this expression being applicable to all mirror settings. The new theory is applied to experimental data collected at the Swiss Light Source Materials Science beamline powder diffractometer for three photon energies under extreme mirror bending conditions using the small-linewidth powder sample Na2Ca3Al2F14.

Three-dimensional birefringence imaging with a microscope tilting-stage. I. Uniaxial crystals

Pajdzik, L.A. — 2006-06-01

The development of a microscope tilting-stage suitable for use with birefringence imaging is described, thus enabling precise three-dimensional birefringence information of uniaxial crystals to be obtained. Equations have been derived for uniaxial crystals in any orientation. The technique enables precise values of the birefringence Δn = ne − no (difference between extraordinary and ordinary refractive index) and orientation of the optic axis to be obtained. The sign of the optical indicatrix may be unambiguously identified. The method is also able to obtain information on preferred orientation in a polycrystalline material. In addition to this, an unknown crystalline material may be identified, or at least classified within a specific group of crystalline materials.

A program for automated optimization of initial crystallization conditions

Ben Haj Abdellatif, T. — 2006-06-01

Protein crystallization is a difficult and time-consuming task, because to obtain a crystal, optimization steps are required almost systematically. A tool that simplifies the optimization of crystallization conditions, and that can be used by any crystallographer to design a crystallization plate and to visualize its content, has become a paramount necessity. A free and open-source application has been developed to automate this task. It is based on a graphical user interface (GUI) that allows a personalized crystallization plate to be designed. All data used and generated are saved in XML documents, which allow reuse of the information. The steps involved in preparing a crystallization plate and the functions of the GUI designed to perform these steps are described. Plans for future development are presented. The program was written in Java. The application and its documentation are available under CeCILL license, which is a Free Software license agreement.

A new apparatus for measuring mechanical properties at moderate confining pressures in a neutron beamline

Covey-Crump, S.J. — 2006-04-01

A simple pressure vessel suitable for use at room temperature has been developed which allows neutron diffraction data to be collected from cylindrical samples of up to 10 mm diameter, at confining pressures of up to 160 MPa, whilst they are also being deformed in compression by the application of a uniaxially symmetric load. The vessel has been commissioned on the ENGIN-X beamline at the ISIS neutron facility (Rutherford Appleton Laboratory, Chilton, UK). The commissioning results show that neutron diffraction data of quality equivalent to that obtained using an identical experiment geometry at room pressure can be acquired using the pressure vessel with only about a factor of two increase in count times.

Solid state chemistry: an introduction. 3rd Edition. By Lesley E. Smart and Elaine A. Moore. Pp. 407. Boca Raton: Taylor and Francis CRC Press, 2005. Price (softcover) USD 69.95. ISBN 0 748 77516 1.

Paufler, P.P. — 2006-04-01

Phase imaging using time-of-flight neutron diffraction

Gutmann, M.J. — 2006-02-01

A technique that allows the spatial distribution of crystallographic phases in the interior of an object to be reconstructed from neutron time-of-flight (TOF) diffraction is described. To this end, the shift of the Bragg peaks due to the so-called `geometrical aberration' is exploited. A collimated incident white beam is used to perform a translational or rotational scan of the object whilst collecting a TOF data set for each sample position or orientation. Depending on the location of any scattering material along the line of the incident beam path through the object, the measured d-spacings of the corresponding Bragg peaks are shifted with respect to their nominal values, which are attained only at the geometrical centre of the instrument. Using a formula that is usually employed to correct for sample offset, the phase distribution along the incident beamline can be directly reconstructed, without the need to perform a tomographic reconstruction. Results are shown from a demonstration experiment carried out on a cylindrical Al container enclosing an arrangement of Cu and Fe rods. On the basis of this formalism, an optimized experimental geometry is described and the potential and limits of this technique are explored, as are its applicability to X-ray and constant-wavelength neutron diffraction.

Energy separation of neutrons scattered at small angles from silicon using time-of-flight techniques

Cheung, J.Y. — 2006-02-01

The time-of-flight technique is used on a small-angle neutron scattering instrument to separate the energies of the scattered neutrons, in order to determine the origin of the temperature-dependent scattering observed from silicon at Q > ∼0.1 Å−1. A quantitative analysis of the results in comparison with the phonon dispersion curves, determined by Dolling using a triple-axis neutron spectrometer, shows that the temperature-dependent scattering can be understood in terms of Umklapp processes whereby neutrons gain energy from phonons.