Open access article in Journal of Applied Crystallography

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.

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.

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.

Crystallography education and training for the 21st century

Kantardjieff, K.A. — 2010-10-01

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.

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.

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.

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.

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

Kutsumizu, S. — 2007-04-21

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

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

Viola, R. — 2007-06-01

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

Hierarchical structure of niobate nanosheets in aqueous solution

Yamaguchi, D. — 2007-04-21

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

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.

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

Bonini, M. — 2007-04-21

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

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

Smolsky, I.L. — 2007-04-21

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

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.

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.

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.

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.

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

Yamada, Y. — 2007-04-21

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

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

Kawai-Hirai, R. — 2007-04-21

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

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

Yano, Y.F. — 2007-04-21

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

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

Pranzas, P.K. — 2007-04-21

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

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

Jiang, Z. — 2007-04-21

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

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

Roth, S.V. — 2007-04-21

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

Scanning X-ray imaging with small-angle scattering contrast

Gourrier, A. — 2007-04-21

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

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

Sugiyama, M. — 2007-04-21

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

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

Chen, S.-H. — 2007-04-21

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

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

Putra, E.G.R. — 2007-04-21

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

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.

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.

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

Shimizu, S. — 2007-04-21

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

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

Betti, F. — 2007-04-21

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

Modelling of bacteriophage capsids and free nucleic acids

Zipper, P. — 2007-04-21

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

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.

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.

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.

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

Huang, T.-W. — 2007-04-21

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

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

Grigoryeva, N.A. — 2007-04-21

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

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.

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.