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Showing papers in "Journal of Applied Crystallography in 1997"


Journal ArticleDOI
TL;DR: L Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.
Abstract: Computer Program Abstracts The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and significant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. CrysL (1985). 18, 189190] and on the World Wide Web at http://www.iucr. ac. uk/journals/jac/software/. Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known. J. App/. CrysL (1997). 30, 565 ORTEP-3 for Windows a version of ORTEP-III with a Graphical User Interface (GUI)

19,468 citations


Journal ArticleDOI
TL;DR: MOLREP as mentioned in this paper is an automated program for molecular replacement which utilizes effective new approaches in data processing and rotational and translational searching, such as automatic choice of all parameters, scaling by Patterson origin peaks and soft resolution cut-off.
Abstract: MOLREP is an automated program for molecular replacement which utilizes effective new approaches in data processing and rotational and translational searching. These include an automatic choice of all parameters, scaling by Patterson origin peaks and soft resolution cut-off. One of the cornerstones of the program is an original full-symmetry translation function combined with a packing function. Information from the model already placed in the cell is incorporated in both translation and packing functions. A number of tests using experimental data proved the ability of the program to find the correct solution in difficult cases.

4,674 citations


Journal ArticleDOI
TL;DR: For outlier discrimination or down-weighting, sample median values have the advantage of being much less outlier-based than sample mean values would be.
Abstract: Experience with a variety of diffraction data-reduction problems has led to several strategies for dealing with mismeasured outliers in multiply measured data sets. Key features of the schemes employed currently include outlier identification based on the values ymedian = median(|Fi|2), σmedian = median[σ(|Fi|2)], and |Δ|median = median(|Δi|) = median[||Fi|2-median (|Fi|2)|] in samples with i = 1, 2 ..... n and n ≥ 2 measurements; and robust/resistant averaging weights based on values of |zi| = |Δi|/max{σmedian, |Δ|median[n/(n−1)]1/2}. For outlier discrimination or down-weighting, sample median values have the advantage of being much less outlier-based than sample mean values would be.

1,263 citations


Journal ArticleDOI
TL;DR: The program ALIGN provides information in its analysis of results to facilitate the understanding of transformations between structurally homologous subunits of protein structures.
Abstract: The alignment and superposition of protein structures are sometimes complicated by the presence of insertions or deletions in one structure or the other. The program ALIGN [Satow, Cohen, Padlan & Davies (1986). J. Mol. Biol. 190, 593–604] was written to address this problem. The program provides information in its analysis of results to facilitate the understanding of transformations between structurally homologous subunits of protein structures.

404 citations


Journal ArticleDOI
TL;DR: A generalized spherical-harmonic description of the texture for polycrystalline materials has been implemented in a multiple-phase/multiple-data-set Rietveld refinement code.
Abstract: A generalized spherical-harmonic description of the texture for polycrystalline materials has been implemented in a multiple-phase/multiple-data-set Rietveld refinement code. It has been tested using two sets of neutron time-of-flight data taken from a standard calcite sample previously used for a round-robin study [Wenk (1991). J. Appl. Cryst. 24, 920–927] and has been shown to give similar texture results as those obtained from individual pole figures. Simultaneous refinement of the calcite crystal structure including anisotropic thermal parameters gives results essentially identical to a recent single-crystal X-ray study.

393 citations


Journal ArticleDOI
TL;DR: The use of oriented quartz single crystals is proposed as an improved internal pressure standard for high-pressure single-crystal diffraction experiments in diamond-anvil cells in this article.
Abstract: The unit-cell parameters of quartz, SiO2, have been determined by single-crystal diffraction at 22 pressures to a maximum pressure of 8.9 GPa (at room temperature) with an average precision of 1 part in 9000. Pressure was determined by the measurement of the unit-cell volume of CaF2 fluorite included in the diamond-anvil pressure cell. The variation of quartz unit-cell parameters with pressure is described by: a −4.91300 (11) = −0.0468 (2) P + 0.00256 (7) P2 − 0.000094 (6) P3, c − 5.40482 (17) = − 0.03851 (2) P + 0.00305 (7) P2 − 0.000121 (6) P3, where P is in GPa and the cell parameters are in angstroms. The volume–pressure data of quartz are described by a Birch–Murnaghan third-order equation of state with parameters V0 = 112.981 (2) a3, KT0 = 37.12 (9) GPa and K′ = 5.99 (4). Refinement of K′′ in a fourth-order equation of state yielded a value not significantly different from the value implied by the third-order equation. The use of oriented quartz single crystals is proposed as an improved internal pressure standard for high-pressure single-crystal diffraction experiments in diamond-anvil cells. A measurement precision of 1 part in 10 000 in the volume of quartz leads to a precision in pressure measurement of 0.009 GPa at 9 GPa.

369 citations


Journal ArticleDOI
TL;DR: DISCUS as discussed by the authors is a tool for the analysis of diffuse scattering and defect structure simulations in Fortran77-based languages, including IF statements and various loops combined with predefined defect types like thermal displacements, waves and microdomains.
Abstract: The program DISCUS is a versatile tool for the analysis of diffuse scattering and for defect structure simulations. The model structure can be created from an asymmetric unit of a unit cell or a complete structure can be read from a file. A Fortran77 style interpreter that includes IF statements and various loops combined with predefined defect types like thermal displacements, waves and microdomains allows one to create all sorts of defect structures. The Fourier-transform segment of the program allows one to calculate neutron as well as X-ray intensities including isotropic temperature factors and anomalous scattering. The calculation of the inverse and difference Fourier transform as well as the Patterson function is also implemented. A model structure can be `fitted' to observed diffuse scattering data by reverse Monte Carlo (RMC) simulations. The RMC segment allows one to model displacive as well as occupational disorder. The program is completely written in Fortran77 and the source code is available via the World Wide Web.

339 citations


Journal ArticleDOI
TL;DR: In this article, a small-angle diffraction with a pulsed neutron source, using time-of-flight analysis to separate neutrons of different wavelengths, offers a very wide simultaneous Q range coupled to good Q resolution.
Abstract: Small-angle diffraction with a pulsed neutron source, using time-of-flight analysis to separate neutrons of different wavelengths, offers a very wide simultaneous Q range coupled to good Q resolution. Data reduction to allow for wavelength-dependent effects may be achieved as a matter of routine. The cold neutron flux available from accelerator-based neutron sources does not yet fully match that of the most intense reactor sources. Simulations show that the performance of proposed future instrumentation would be largely complementary to that of the best fixed-wavelength instruments.

273 citations


Journal ArticleDOI
TL;DR: In this article, a generalized version of the indirect Fourier transformation method is proposed to determine the form factor and the structure factor simultaneously, which can be seen as a generalization of the Fourier transform.
Abstract: Indirect Fourier transformation is a well established method for the evaluation of small-angle scattering data. This technique, however, is restricted to dilute solutions, as for higher concentrations particle interactions can no longer be neglected. As the scattering intensity contains intra- and interparticle scattering contributions, the evaluation of scattering data is no longer just the solution of a linear weighted least-squares problem because the scattering intensity can, under certain conditions, be written as the product of the particle form factor and the so-called structure factor, which leads to a highly non-linear problem. In this paper a global evaluation technique including the structure factor is presented so that it is possible to determine the form factor and the structure factor simultaneously. This technique can be understood as a generalized version of the indirect Fourier transformation method. Like in the indirect Fourier transformation, there are no models or no analytical restrictions used for the form factor, and the structure factor is parameterized with up to four parameters for a given interaction model. A simultaneous determination of these two functions is possible due to the different analytical behavior of these functions, which also leads in most cases to the existence of a global minimum in the parameter surface. An algorithm to solve this nonlinear least-squares problem has been developed and applied to simulated data for a variety of different uncharged systems.

267 citations


Journal ArticleDOI
TL;DR: In this article, the geometrical and resolution corrections that occur in the measurement of the integrated intensities of surface diffraction rods for the case of a six-circle diffractometer are derived.
Abstract: The geometrical and resolution corrections are derived that occur in the measurement of the integrated intensities of surface diffraction rods for the case of a six-circle diffractometer. Since the six-circle geometry entails as special cases the five-circle and the z-axis diffractometers, the results are valid for these geometries as well. The derivations are valid for any incoming or outgoing angle of the X-ray beam, and are particularly important for measurements at large perpendicular momentum transfer. Expressions are derived for the integrated intensity from rocking scans, from stationary measurements and from reflectivity data. With all correction factors known, it is possible to derive the structure factors with a common scale factor from all these types of scans. It is expected that area detectors combined with stationary measurements will find widespread use in the surface X-ray diffraction community.

254 citations



Journal ArticleDOI
TL;DR: In this paper, a comparison of the accuracy and the merging R factor (Rmerge) of artificially created X-ray data sets is made, and it is demonstrated that Rmerge is a poor predictor for the precision of X-rays.
Abstract: By comparison of the accuracy and the merging R factor (Rmerge) of artificially created X-ray data sets, it is demonstrated that Rmerge is a poor predictor for the precision of X-ray data. The more often a given reflection is observed, the more precise the average intensity is, whereas Rmerge has a tendency to be higher at higher data redundancy.

Journal ArticleDOI
TL;DR: In this article, a fast and reliable algorithm was developed for auto-indexing oscillation images, where the observed reflection positions were used to compute the corresponding reciprocal-lattice vectors assuming a stationary crystal.
Abstract: A fast and reliable algorithm has been developed for auto-indexing oscillation images. The observed reflection positions are used to compute the corresponding reciprocal-lattice vectors assuming a stationary crystal. These vectors are then projected onto a chosen direction. The projections are subjected to a one-dimensional Fourier analysis. A large Fourier term will be found that has a periodicity corresponding to the interplanar distance if the chosen direction happens to be perpendicular to a set of widely separated reciprocal-lattice planes. Exploration of such directions over a hemisphere establishes the best potential basis vectors of the real cell. The program has successfully determined the lengths and directions of basis vectors for numerous unit cells having cell dimensions ranging from 16 to 668 A and oscillation ranges from 0.2 to 2.0°.

Journal ArticleDOI
TL;DR: In this article, a modified application of the variance method, using the pseudo-Voigt function as a good approximation to the X-ray diffraction profiles, is proposed in order to obtain microstructural quantities such as the mean crystallite size and root-mean-square (r.m.s.) strain.
Abstract: A modified application of the variance method, using the pseudo-Voigt function as a good approximation to the X-ray diffraction profiles, is proposed in order to obtain microstructural quantities such as the mean crystallite size and root-mean-square (r.m.s.) strain. Whereas the variance method in its original form is applicable only to well separated reflections, this technique can be employed in the cases where there is line-profile overlap. Determination of the mean crystallite size and r.m.s. strain for several crystallographic directions in a nanocrystalline cubic sample of 9-YSZ (yttria-stabilized zirconia) has been performed by means of this procedure.

Journal ArticleDOI
TL;DR: In this paper, the Rietveld program XRS-82 and the profile extraction program ALLHKL have been modified to allow flat imaging-plate powder diffraction data to be refined.
Abstract: The combination of intense X-ray synchrotron radiation and an imaging-plate area detector makes it possible to extract real-time structural information using Rietveld refinement of individual time slices. Powder diffraction data from capillary samples were collected using a flat imaging plate mounted perpendicular to, or at an oblique angle to, the incoming beam. Owing to the geometry of the experiments, several factors must be taken into account when Rietveld refinement of powder diffraction data obtained using a flat imaging plate is performed: (i) nonequal step sizes are obtained when the diffraction profiles are extracted; (ii) the refined zero-point correction is different from that for conventional diffraction geometry; (iii) the sample-detector distance is not constant, requiring a modified geometric term in the Lorentz factor; (iv) the geometric contribution to the instrumental resolution function must be considered. The geometric factors have been derived and are discussed. The Rietveld program XRS-82 and the profile extraction program ALLHKL have been modified to allow flat imaging-plate powder diffraction data to be refined. The Rietveld refinement of powder diffraction data of α-quartz collected using a 30 s exposure is presented. LaB6 powder diffraction data were collected using various settings. The profile variation with angle and the resolution function are described. Data were collected up to sin θ/λ = 1.29 A−1 (d values down to 0.39 A) using high energy and with the imaging plate inclined at an angle to the incoming beam.

Journal ArticleDOI
TL;DR: In this paper, a small-angle X-ray scattering (SAXS) system based on a pinhole camera with rotating anode and area detector is presented, and first applications to the study of bone and wood are reported.
Abstract: Many biological materials, like bone or wood, are hierarchically organized and optimized at all levels for their specific mechanical function. At the lowest level, these materials are fiber composites, where the fiber direction as well as the size of the individual components varies considerably with position inside a given specimen. For bone or wood, some of these parameters can be readily obtained by small-angle X-ray scattering (SAXS) in a position-resolved way. A scanning-SAXS system based on a pinhole camera with rotating anode and area detector is presented, and first applications to the study of bone and wood are reported.

Journal ArticleDOI
TL;DR: In this article, the orientation distribution of a textured polycrystal has been determined from a few individual pole figures of lattice planes hkl, measured by X-ray or neutron diffraction.
Abstract: The orientation distribution of a textured polycrystal has been traditionally determined from a few individual pole figures of lattice planes hkl, measured by X-ray or neutron diffraction. A new method is demonstrated that uses the whole diffraction spectrum, rather than extracted peak intensities, by combining ODF calculation with Rietveld crystal structure refinement. With this method, which is illustrated for a synthetic calcite texture, it is possible to obtain quantitative texture information from highly incomplete pole figures and regions of the diffraction spectrum with many overlapping peaks. The approach promises to be advantageous for low-symmetry compounds and composites with complicated diffraction spectra. The method is particularly elegant for time-of-flight neutron diffraction, saving beam time by using small pole-figure regions and many diffractions.

Journal ArticleDOI
TL;DR: The crystal structures of rutile and its high-pressure polymorphs have been studied by X-ray powder diffraction in the pressure range up to 60 GPa as mentioned in this paper.
Abstract: The crystal structures of rutile (TiO2) and its high-pressure polymorphs have been studied by X-ray powder diffraction in the pressure range up to 60 GPa. At 12 GPa, rutile transforms to a phase with the baddeleyite (ZrO2) structure. Upon decompression, this phase transforms at 7 GPa to another phase with the α-PbO2 structure. At ambient conditions, the α-PbO2-type phase is 2.1 (3)% denser than rutile and the baddeleyite-type phase is 11.3 (9)% denser than rutile. In the pressure range of the rutile-to-baddeleyite transition, the difference in density between the two phases is 9.75 (15)%. The zero-pressure bulk moduli, as determined from the equation of state, are 230 (20), 260 (30) and 290 (20) GPa for rutile, the α-PbO2-type phase and the baddeleyite-type phase, respectively.

Journal ArticleDOI
TL;DR: In this paper, the authors describe the small-angle scattering beamline built at the Brazilian Synchrotron Light Laboratory (LNLS) using an elastically bent gold-plated cylindrical mirror.
Abstract: This paper describes the small-angle scattering beamline built at the Brazilian Synchrotron Light Laboratory (LNLS). Vertical focusing of the synchrotron beam is achieved by an elastically bent gold-plated cylindrical mirror. An asymmetric cut curved triangle-shaped silicon single crystal (111 reflection) is used for monochromatization and horizontal focusing. The mirror, monochromator optics and 2θ arm were designed to cover the spectral range between 1.0 and 2.0 A. Three slit sets, a secondary photon shutter, two beam monitors, filters and absorbers, a multi-sample holder, a vacuum path, a beam-stopper and a set of detectors are the basic components of the workstation. The stepping motors are equipped with specially designed encoders. All mechanical and pneumatic movements and detectors can be remotely controlled using a direct panel or a PC.

Journal ArticleDOI
TL;DR: In this article, a beamline for small-angle X-ray scattering (SAXS) has been constructed and is presently under final commissioning at the 2'GeV storage ring ELETTRA.
Abstract: A new beamline for small-angle X-ray scattering (SAXS) has recently been constructed and is presently under final commissioning at the 2 GeV storage ring ELETTRA. It has been designed specifically for time-resolved studies of non-crystalline and fibrous materials and has been optimized for small-angle scattering measurements. The beamline operates with a SAXS resolution between 10 and about 1400 A in d spacing (at 8 keV) and has been optimized with respect to high flux at the sample [of the order of 1013 photons s−1 for 8 keV photons (2 GeV, 400 mA)]. Soon it will be possible to perform simultaneously wide-angle diffraction measurements in the d-spacing range 1.2–8 A (at 8 keV). In order to allow time-resolved (resolution ~1 ms) small-angle scattering measurements, a high-power 57-pole wiggler is used as the beamline source. From its beam, one of three discrete energies, 5.4, 8 and 16 keV, can be selected with a double-crystal monochromator, which contains three pairs of asymmetrically cut plane Si(111) crystals. Downstream, the beam is focused horizontally and vertically by a toroidal mirror. Commissioning tests of this new SAXS beamline showed that all design parameters have been realized.

Journal ArticleDOI
TL;DR: Out outliers may be identified, remedial action taken, and the overall refinement improved upon, as well as nonlinear least-squares refinement, minimiz© 1997 International Union of Crystallography.
Abstract: Computer Program Abstracts The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and significant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal lJ. Appl. Cryst. (1985). 18, 189-190]. J. Appl. Cryst. (1997). 30, 84 UNITCELL: a nonlinear least-squares program for cell-parameter refinement implementing regression and deletion diagnostics T. J. B. HOLLAND AND S. A. T. REDFERN Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, England. E-mail: tjbh @ esc.cam.ac.uk (Received 25 July 1996; accepted 4 October 1996) The crystallographic problem: During the refinement of unit-cell parameters from the observed positions of Bragg reflections in powder diffraction patterns, errors in the indexing and measurement of reflections are usually identified by their associated large residuals (e.g. 20ob s -20calc ). A more robust approach to the identification of such outliers in a data set is to employ regression diagnostics (Belsey, Kuh & Welsh, 1980; Powell, 1985; Holland & Redfern, 1997). The program UN/TCELL refines cell parameters by minimizing residuals in the experimentally determined Bragg position (in terms of 20hk I, d spacing dhk I or energy Ebkl) using a nonlinear leastsquares method. Regression diagnostics are provided that give information on the sensitivity of the refinement result to individual reflection positions (the leverage of each datum), as well as deletion diagnostics that indicate how deleterious each observed position is to the overall fit and automatically compute the effect of removing individual potentially deleterious observations from the data set. Hence, outliers may be identified, remedial action taken, and the overall refinement improved upon. Method of solution: From an indexed list of Bragg positions (in Qhkl, 20hkl, dhkl or Ehk I provided in the input data file), UNITCELL refines the unit-cell parameters by first obtaining an initial estimate of the cell parameters from minimization of residuals in Qhkl by linear least squares [given the crystal system and following Kelsey (1964)] and then conducting nonlinear least-squares refinement, minimiz© 1997 International Union of Crystallography Printed in Great Britain all rights reserved ing the residuals in the measured (or other user-specified) variable following the approach of Marquardt [as described by Bevington & Robinson (1992)]. This two-step approach therefore requires no initial guess for the cell parameters. The program then computes regression diagnostics for each reflection, determining its Hat (leverage or influence on the calculated parameters), the change in standard error of the residuals obtained by removing it from the data set (how harmful it is to the fit), the magnitude of its residual corrected for leverage, the influence it has on its own calculated position (which is large if it is an outlier), and the change expected in each calculated cell parameter should the reflection be removed from the data set. Used together, these diagnostics are particularly useful in assessing any individual sources of error in a cell-parameter refinement. The user has the option of outputting diagnostics for every datum, or for a limited number of data points that lie beyond statistically defined cutoff values that indicate that they may be either influential or deleterious to the fit. Software environment: UNITCELL will run under both PC Windows and Apple Macintosh system 6 onwards. The Macintosh version was developed using Symantec Think Pascal and the PC Windows version was implemented using Borland's Turbo Pascal for Windows. The Macintosh version is designed to be interactive with a user-friendly graphical user interface. The crystal system, data type ( Qhkl, 20 hkl, dhkl or Ehkl), wavelength or 20 angle, quantity to be minimized in the refinement (residuals in Qhkl, 2ehkl, dhkl or Ehkl) and input and output files are specified via an interactive input screen, with menu options. The PC Windows version is less elaborate, these specifications being incorporated within the first few lines of the input data file. The output results are displayed in their own text window, as well as being saved to a user-specified output file. The output file for the PC Windows version is plain text; the output file for the Macintosh version can be written in one of seven user-specified editor formats (MS Word, EDIT II, Vantage/McSink, BBEdit, QEDM, Generic Text or TeachText). Hardware environment: UNITCELL will run on any Apple Macintosh with or without FPU (both versions available; PPC users should employ the non-FPU version). The Windows version has been run on PC-compatible computers from 386 upwards. The executable PC Windows version is 80 kbytes. The source code comprises some 1991 lines of Pas-

Journal ArticleDOI
TL;DR: In this article, a technique for improving protein-crystal size by slowing down the crystallization process is described, which is achieved by the setting up of a vapour-diffusion experiment with a layer of oil placed above the reservoir.
Abstract: The process of protein crystallization often takes place too rapidly, thus producing showers of crystals instead of large single crystals. A novel technique for improving protein-crystal size by slowing down the crystallization process is described. This is achieved by the setting up of a vapour-diffusion experiment with a layer of oil placed above the reservoir. The oil acts as a barrier between the reservoir and the crystallization drop, but water vapour diffuses slowly through the layer of oil. The type of oil and the thickness of the oil layer situated above the reservoir will dictate the rate of vapour diffusion and consequently the speed of crystallization. This technique reduces the number of crystals grown and increases their size.

Journal ArticleDOI
TL;DR: The FOCUS method as mentioned in this paper combines automatic Fourier recycling with a specialized topology search specific to zeolites, which can be described as having three-dimensional four-connected framework structures.
Abstract: The FOCUS method, in which both crystal chemical information and powder diffraction data are included in the structure determination process, is presented. FOCUS combines automatic Fourier recycling with a specialized topology search specific to zeolites, which can be described as having three-dimensional four-connected framework structures. The capabilities of FOCUS have been tested with seven examples of medium to high complexity. The method was then applied to three novel zeolite structures and a promising model could be obtained in each case. Experience shows that the approach of using chemical and geometric knowledge can compensate for some of the information that is lost as a result of the overlap problem. At the same time, there is an intrinsic disadvantage: any method based on assumptions of certain structural properties is also limited to materials which conform to these assumptions. Examples which show the consequences of relaxing the structural assumptions are also given.

Journal ArticleDOI
TL;DR: The design, development and performance of the small-angle diffractometer (SAD) at the Intense Pulsed Neutron Source (IPNS) at Argonne National Laboratory are described in this paper.
Abstract: The design, development and performance of the time-of-flight (TOF) small-angle diffractometer (SAD) at the Intense Pulsed Neutron Source (IPNS) at Argonne National Laboratory are described. Similar TOF-SANS instruments are in operation at the pulsed neutron sources at Los Alamos National Laboratory, USA, at Rutherford Appleton Laboratory, England, and at KEK, Japan. These instruments have an advantage by comparison with their steady-state counterparts in that a relatively wide range of momentum transfer (q) can be monitored in a single experiment without the need to alter the collimation or the sample-to-detector distance. This feature makes SANS experiments easy and very effective for studying systems such as those undergoing phase transitions under different conditions, samples that cannot be easily reproduced for repetitive experiments, and systems under high temperature, pressure or shear. Three standard samples are used to demonstrate that the quality of the SANS data from SAD is comparable with those from other established steady-state SANS facilities. Two examples are given to illustrate that the wide q region accessible in a single measurement at SAD is very effective for following the time-dependent phase transitions in paraffins and temperature- and pressure-dependent phase transitions in model biomembranes.

Journal ArticleDOI
TL;DR: In this article, it is shown that grazing-incidence small-angle X-ray scattering (GISAXS) is a new experimental technique that combines both grazing incidence and scattering at low angles.
Abstract: It is shown that grazing-incidence small-angle X-ray scattering (GISAXS) is a new experimental technique that combines both grazing incidence and scattering at low angles The experiments are carried out at or near the critical angle: the result is a considerably enhanced surface sensitivity It allows morphological characterization of aggregates deposited or gathered on a fiat substrate, such as silicon wafer or Coming glass The full potential of this technique is realized when using a synchrotron source (flux, collimation and choice of wavelength in order to avoid fluorescence or to perform anomalous measurements) and when patterns are recorded with two-dimensional detectors: gas detectors or imaging plates (IPs) It is then possible to study the anisotropic shape of the scattering pattern and to determine the sizes of the aggregates Results are presented for gold clusters deposited on a silicon wafer covered by a carbon sublayer in order to make a comparison with transmission electron microscopy and with scanning probe microscopy Other examples are presented in order to highlight the advantages of such a technique applied to small inclusions in thin surface layers

Journal ArticleDOI
TL;DR: In this article, a new approach based on the Monte Carlo method of solving molecular crystal structures from full-pattern profile analysis of powder diffraction data is described, which represents a significant advance on previous Monte Carlo methods in that it permits the solution of flexible (i.e. with variable bond lengths, bond and torsion angles) molecules.
Abstract: A new approach based on the Monte Carlo method of solving molecular crystal structures from full-pattern profile analysis of powder diffraction data is described. The new approach represents a significant advance on previous Monte Carlo methods in that it permits the solution of flexible (i.e. with variable bond lengths, bond and torsion angles) molecules. It does this by not only allowing random rotations and translations of individual atoms and rigid-body fragments comprising an asymmetric unit, but by permitting changes of internal configuration of stereochemically constrained moieties. The last option was crucial in the case of the structure solution of poly(ethylene oxide)3:LiN(SO2CF3)2, containing 25 non-H atoms in the asymmetric unit. Using a specifically designed computer code the atomic positions of the flexible poly(ethylene oxide) [(CH2–CH2–O)n] chain and imide N(SO2CF3)2− group are described in terms of bond lengths, angles and torsion angles, offering a means of introducing chemical constraints which, in turn, significantly reduce the number of parameters to be varied in a random fashion. Furthermore, tests for reasonable inter-fragment distances avoid the unnecessary calculation of chemically unreasonable structures. A detailed account of the random-search procedure combined with simulated annealing is given.

Journal ArticleDOI
TL;DR: The ORNL Ultra-Small-Angle Neutron Scattering (USANS) facility at the High Flux Isotope Reactor (HIFR) has been recently upgraded, using the Bonse-Hart technique.
Abstract: The ORNL Ultra-Small-Angle Neutron Scattering (USANS) facility at the High Flux Isotope Reactor (HIFR) has been recently upgraded, using the Bonse–Hart technique. Si(111) triple-bounce channel-cut single crystals have been used for both the monochromator and analyzer. The total width of the rocking curve of the analyzer is about 1.6′′ and the wavelength of the primary neutron beam is 2.59 A. It has been demonstrated that, owing to the low neutron absorption of silicon, the wings of the rocking curve are generally contaminated by neutrons propagating and diffracting inside the walls of channel-cut crystals. This parasitic intensity has been eliminated by the cutting of a groove in the long wall and the insertion of a cadmium absorber (0.6 mm thick). This modification effectively suppresses the wings of the rocking curve by over two orders of magnitude and thus dramatically improves the sensitivity of the diffractometer. The upgraded facility has been tested with several samples, including a polystyrene latex with a radius of 2.50 × 104 A as determined by optical microscopy. The average radius calculated from USANS data is 2.48 × 104 A, in excellent agreement with independently determined dimensions. The minimum accessible scattering vector of the upgraded USANS facility is Qmin ≃ 2 × 10−5 A−1, which corresponds to a maximum resolvable real-space dimension of 2π/Qmin ≃ 3 × 105 A (30 μm).

Journal ArticleDOI
TL;DR: The results of the structural determination of Li 2 MnO 3 from X-ray powder diffraction data and the refinement by the Rietveld technique are presented in this paper.
Abstract: The results of the structural determination of Li 2 MnO 3 from X-ray powder diffraction data and the refinement by the Rietveld technique are presented. The Li 2 MnO 3 structure has a monoclinic cell with space group C2/m (Z = 4) and cell parameters a = 4.9246(1), b= 8.5216 (1), c = 5.0245 (1) A, β=109.398 (1)°; the refinement with 14 structural parameters for 165 reflections in the pattern leads to R wp = 17.61%, R p = 13.25%, R B = 7.07% and S = 3.52. Such a solution agrees with a single-crystal structure determination previously reported in the literature and allows other hypotheses to be rejected.

Journal ArticleDOI
TL;DR: In this paper, a paracrystalline one-dimensional Hosemann model is used for line profile simulation and matching on the basis of a paracelline model.
Abstract: Line-profile simulation and matching on the basis of a paracrystalline one-dimensional Hosemann model provides a promising approach to the analysis of line broadening. Results of analysis using X-ray wide-angle data of polymers and metallic samples are compared with Warren–Averbach multiple-order and single-order methods. Various column-length-distribution functions are also used for better agreement with the experimental profiles.

Journal ArticleDOI
TL;DR: ASSA as discussed by the authors is a program for 3D rendering and interactive model refinement using PHIGS+ standard for the three-dimensional solid rendering and XView and XLib libraries for the menu-driven user interface.
Abstract: A program for three-dimensional rendering and interactive model refinement, ASSA, is presented. The program permits the simultaneous display and manipulation of low-resolution envelope models obtained from solution-scattering data and the crystallographic or electron microscopic models in the Brookhaven Protein Data Bank format. ASSA is coupled with the shape-determination program of Svergun, Volkov, Kozin, Stuhrmann, Barberato & Koch [J. Appl. Cryst. (1997). 30, 000–000], thus allowing one to monitor the shape determination process in real time. The program ASSA is written in C using the PHIGS+ standard for the three-dimensional solid rendering and the XView and XLib libraries for the menu-driven user interface. The system runs on a Sun SPARC ZX-20 workstation; a simplified IBM-PC version is also available.