Influence of surface relaxations on X-ray intensities of microcrystals

1995 ◽  
Vol 210 (6) ◽  
Author(s):  
R. B. Neder
Keyword(s):  
Volume Fraction ◽  
Structure Refinement ◽  
Perfect Crystal ◽  
Data Sets ◽  
Near Surface ◽  
X Ray ◽  
Simulation Techniques ◽  
Small Crystals ◽  
Structure Simulation ◽  
Standard Structure

AbstractThe influence of surface relaxations on the intensity of microcrystals was investigated. Since the volume fraction of near surface atoms becomes appreciable for submicrometer crystals, it is important to estimate whether observed intensities of submicrometer crystals can be interpreted with standard structure refinement methods or whether surface relaxations produce a significant deviation from the intensities of the perfect crystal.Structure simulation techniques were applied in order to calculate the intensity of microcrystals of various sizes. Different models of surface relaxations were applied. Structure refinements on the data sets calculated for these models showed that submicrometer crystals down to 0.5 μm in diameter are not affected by surface relaxations. Smaller crystals below 0.1 μm in diameter are significantly affected by surface relaxations. Great care will have to be taken when refining observed intensities of these small crystals.

Comparative study of X-ray charge-density data on CoSb3

2013 ◽  
Vol 69 (6) ◽  
pp. 570-582 ◽  
Author(s):  
Mette Stokkebro Schmøkel ◽  
Lasse Bjerg ◽  
Finn Krebs Larsen ◽  
Jacob Overgaard ◽  
Simone Cenedese ◽  
...  
Keyword(s):  
Charge Density ◽  
High Performance ◽  
Theoretical Data ◽  
High Energy ◽  
Data Sets ◽  
High Symmetry ◽  
X Ray ◽  
Structure Factors ◽  
Small Crystals ◽  
Density Analysis

CoSb3is an example of a highly challenging case for experimental charge-density analysis due to the heavy elements (suitability factor of ∼0.01), the perfect crystallinity and the high symmetry of the compound. It is part of a family of host–guest structures that are potential candidates for use as high-performance thermoelectric materials. Obtaining and analysing accurate charge densities of the undoped host structure potentially can improve the understanding of the thermoelectric properties of this family of materials. In a previous study, analysis of the electron density gave a picture of covalent Co–Sb and Sb–Sb interactions together with relatively low atomic charges based on state-of-the-art experimental and theoretical data. In the current study, several experimental X-ray diffraction data sets collected on the empty CoSb3framework are compared in order to probe the experimental requirements for obtaining data of high enough quality for charge-density analysis even in the case of very unsuitable crystals. Furthermore, the quality of the experimental structure factors is tested by comparison with theoretical structure factors obtained from periodic DFT calculations. The results clearly show that, in the current study, the data collected on high-intensity, high-energy synchrotron sources and very small crystals are superior to data collected at conventional sources, and in fact necessary for a meaningful charge-density study, primarily due to greatly diminished effects of extinction and absorption which are difficult to correct for with sufficient accuracy.

Diffuse X-Ray Scattering Study of Defects Created by KeV Ion Implants In Si

1996 ◽  
Vol 439 ◽  
Author(s):  
P. J. Partyka ◽  
R. S. Averback ◽  
K. Nordlund ◽  
I. K. Robinson ◽  
D. Walko ◽  
...  
Keyword(s):  
Computer Simulation ◽  
Irradiation Damage ◽  
Complex Nature ◽  
Computational Framework ◽  
Near Surface ◽  
X Ray ◽  
Simulation Techniques ◽  
X Ray Scattering ◽  
Surface Measurements ◽  
Ray Scattering

AbstractDiffuse x-ray scattering (DXS) and computer simulation techniques were employed to investigate the defect structure produced in Si by low keV ion and MeV electron irradiations. DXS measurements were performed for keV Ga and He implants, demonstrating the ability of the technique to provide both bulk and near-surface measurements at defect concentrations of about 1000 ppm. A rigorous analysis of these results is complicated due to the complex nature of the ion damage in Si. A computer simulation framework is developed to aid in the analysis of this data. In this technique, defects are simulated and their strain fields are calculated by simply relaxing the atoms around the defect to their equilibrium positions. The diffuse scattering is then calculated from the strain field, and the results are compared to the experimental measurements. Computer simulations are presented here only for the case of electron irradiation damage and compared to published measurements. Application of the technique to more complicated structures is planned and should pose no serious problems in the computational framework already developed.

Characterization of Reactive Ion Etch Damage in GaAs by Triple Crystal X-Ray Diffraction

1993 ◽  
Vol 324 ◽  
Author(s):  
Victor S. Wang ◽  
Richard J. Matyi ◽  
Karen J. Nordheden
Keyword(s):  
Bias Voltage ◽  
Diffuse Scattering ◽  
Reciprocal Lattice ◽  
Surface Region ◽  
Perfect Crystal ◽  
X Ray Diffraction ◽  
Reciprocal Lattice Point ◽  
Near Surface ◽  
X Ray ◽  
Imperfect Crystal

AbstractTriple crystal x-ray diffraction (TCXD) is a non-destructive structural characterization tool capable of the separation and direct observation of the dynamic (perfect crystal) and the kinematic (imperfect crystal) components of the total intensity diffracted by a crystal. Specifically, TCXD can be used to measure the magnitude of the diffuse scattering arising from defects in the crystal structure in the immediate vicinity of a reciprocal lattice point. In this study, the effects of BC13 reactive ion etching (RIE) on the near-surface region of GaAs were investigated by analyzing the changes in the diffuse scattering using both the symmetric 004 reflection as well as the highly asymmetric and more surface sensitive 113 reflection. While the results from the 004 reflections revealed little difference between the unetched and the BC13-etched samples, maps of the diffracted intensity around the 113 reflections showed an unexpected and reproducible decrease in the extent of the diffuse scattering in the transverse direction (perpendicular to the < 113 > direction) as the RIE bias voltage was increased. This decrease suggests that the degree of etch damage induced in the GaAs near-surface region is reduced with increasing bias voltage and ion energy. Additionally, the symmetry and orientation of the kinematic scattering was altered. Possible mechanisms for these results willbe discussed.

Microstructure and Oxidation of a Cast Nickel Aluminide Alloy

2002 ◽  
Vol 753 ◽  
Author(s):  
D. Y. Lee ◽  
M. L. Santella ◽  
I. M. Anderson ◽  
G. M. Pharr
Keyword(s):  
Nickel Aluminide ◽  
Volume Fraction ◽  
Surface Region ◽  
Oxidation Products ◽  
Al Alloy ◽  
X Ray Diffraction ◽  
Multivariate Statistical ◽  
Near Surface ◽  
X Ray ◽  
Spectrum Imaging

ABSTRACTSpecimens of the cast Ni3Al alloy IC221M were annealed in air at 900°C to examine the effects of oxidation and thermal aging on the microstructure. The alloy is comprised of a dendritically solidified γ-γ′ matrix containing γ+Ni5Zr eutectic colonies in the interdendritic regions. Microstructures of aged specimens were examined by optical microscopy and energy dispersive X-ray (EDX) spectrum imaging in the scanning electron microscope (SEM). Two primary changes in the microstructures were observed: (1) there is considerable homogenization of the cast microstructures with aging, and (2) the volume fraction of the γ+Ni5Zr eutectic decreases. Oxidation products were identified using x-ray diffraction and EDX spectrum imaging with multivariate statistical analysis (MSA). During the initial stages of oxidation, the first surface oxide to form is mostly NiO with small amounts of Cr2O3, ZrO2, NiCr2O4, and θ-Al2O3. Initially, oxidation occurs primarily in the interdendritic regions due to microsegregation of alloying elements during casting. With further aging, a continuous film of α-Al2O3 forms immediately beneath the surface that eventually evolves into a double layer of α-Al2O3 and NiAl2O4. Although these oxides are constrained to the near surface region, others penetrate to greater depths facilitated by oxidation of the γ+Ni5Zr eutectic colonies. These oxides appear in the microstructure as long, thin spikes of ZrO2 surrounded by a thin sheath of Al2O3.

scholarly journals Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase

2015 ◽  
Vol 71 (8) ◽  
pp. 1072-1077 ◽  
Author(s):  
Mats Ohlin ◽  
Laura von Schantz ◽  
Tobias E. Schrader ◽  
Andreas Ostermann ◽  
Derek T. Logan ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Structure Refinement ◽  
Carbohydrate Binding ◽  
Initial Structure ◽  
Data Sets ◽  
Rhodothermus Marinus ◽  
Structural Determinants ◽  
X Ray ◽  
Carbohydrate Binding Modules ◽  
Hydrolyzing Enzymes

Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that bind specific types of carbohydrates. Ultra high-resolution X-ray crystallographic studies of CBMs have helped to decipher the basis for specificity in carbohydrate–protein interactions. However, additional studies are needed to better understand which structural determinants confer which carbohydrate-binding properties. To address these issues, neutron crystallographic studies were initiated on one experimentally engineered CBM derived from a xylanase, X-2 L110F, a protein that is able to bind several different plant carbohydrates such as xylan, β-glucan and xyloglucan. This protein evolved from a CBM present in xylanase Xyn10A ofRhodothermus marinus. The protein was complexed with a branched xyloglucan heptasaccharide. Large single crystals of hydrogenous protein (∼1.6 mm3) were grown at room temperature and subjected to H/D exchange. Both neutron and X-ray diffraction data sets were collected to 1.6 Å resolution. Joint neutron and X-ray refinement usingphenix.refineshowed significant density for residues involved in carbohydrate binding and revealed the details of a hydrogen-bonded water network around the binding site. This is the first report of a neutron structure of a CBM and will add to the understanding of protein–carbohydrate binding interactions.

scholarly journals Temperature dependence of Uiso constraints in riding hydrogen treatments

2014 ◽  
Vol 70 (a1) ◽  
pp. C286-C286
Author(s):  
Jens Luebben ◽  
Simon Grabowsky ◽  
Alison Edwards ◽  
Wolfgang Morgenroth ◽  
George Sheldrick ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Structure Refinement ◽  
Heavy Atom ◽  
Data Sets ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Structure Determinations ◽  
Thermal Displacements ◽  
Conventional Structure ◽  
Oniom Approach

"Anisotropic parametrisation of the thermal displacements of hydrogen atoms in single-crystal X-ray structure refinement is not possible with independent atom model (IAM) scattering factors. This is due to the weak scattering contribution of hydrogen atoms. Only when aspherical scattering factors are used can carefully measured Bragg data provide such information. For conventional structure determinations parameters of ""riding"" hydrogen atoms are frequently constrained to values of their ""parent"" heavy atom. Usually values of 1.2 and 1.5 times X-U_eq are assigned to H-U_iso in these cases. Such constraints yield reasonable structural models for room-temperature data. However, todays small molecule X-Ray diffraction experiments are usually carried out at significantly lower temperatures. To further study the temperature dependence of ADPs we have evaluated several data sets of N-Acetyl-L-4-Hydroxyproline Monohydrate at temperatures ranging from 9 K to 250 K. Methods compared were HAR [1], Invariom refinement [2], time-of-flight Neutron diffraction and the TLS+ONIOM approach [3]. In the TLS+ONIOM approach non-hydrogen ADPs from Invariom refinement provided ADPs for the TLS-fit. Hydrogen atoms in all methods were grouped and analyzed according to their Invariom name. We reach a good agreement of the temperature dependence of H-U_iso/X-U_eq. At very low temperatures the ratio H-U_iso/X-U_eq can be as high as 4, e.g. for Hydrogen attached to a sp3 carbon atom with three non-Hydrogen atom neighbors. Since all methods consistently show that the H-U_iso/X-U_eq ratio is temperature dependent, this effect should be taken into account in conventional structure determinations."

Profile agreement indices in Rietveld and pattern-fitting analysis

1990 ◽  
Vol 23 (6) ◽  
pp. 462-468 ◽  
Author(s):  
R. J. Hill ◽  
R. X. Fischer
Keyword(s):  
Crystal Structure ◽  
Signal To Noise Ratio ◽  
Structure Refinement ◽  
Data Sets ◽  
Structure Model ◽  
Signal To Noise ◽  
Neutron Data ◽  
Reduction Stage ◽  
X Ray ◽  
Diffraction Patterns

Two definitions of profile agreement indices are now in common use for estimating the degree of fit in Rietveld refinement and in structure-independent pattern-fitting methods of powder diffraction analysis. In the original program written by Rietveld, the background was subtracted and the `non-peak' regions of the pattern were removed from further consideration in a preliminary data-reduction stage prior to Structure refinement. However, the agreement indices used in many of the more recent programs retain the background counts in the observed step intensities and include all portions of the pattern in the sums. These latter definitions are strongly dependent on the signal-to-noise ratio and on the relative amount of `background-only' regions and do not, therefore, provide a sound basis for comparing the degree of fit of peak profile and crystal structure model refinements in the general case. The extent of this dependence is illustrated quantitatively using conventional and synchrotron X-ray and constant-wavelength and time-of-flight neutron data sets with different inherent background levels and peak densities. The unweighted background-corrected peak-only profile agreement index R′ p = Σ i |Y io − Y ic|/Σ i |Y io −Y ib | (and, to a lesser extent, its weighted equivalent) is recommended as the most appropriate criterion of fit for comparative work between diffraction patterns of all kinds.

Powder X-Ray Structure Refinement Applying a Theory for Particle Statistics

2013 ◽  
Vol 203-204 ◽  
pp. 3-8 ◽  
Author(s):  
Takashi Ida
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Likelihood Estimation ◽  
Data Sets ◽  
Powder Diffraction Data ◽  
Diffraction Intensity ◽  
X Ray ◽  
Statistical Errors ◽  
Particle Statistics

A new method for analysis of powder diffraction intensity data recently developed by the author has been modified to include the effects of possible statistical errors in the goniometer angle 2Θ. The analytical method is based on the maximum-likelihood estimation. Structure parameters refined by the method for fluorapatite Ca5(PO4)3F, anglesite PbSO4and barite BaSO4 have become closer to those obtained by single-crystal structure analyses than the results obtained by applications of a conventional Rietveld refinement to the same powder diffraction data, similarly to the previous analyses, where the errors in 2Θ are not included. The statistical errors about 2Θ are estimated at Δ2Θ = 0.0030º, 0.00099º and 0.0036º from the powder diffraction data sets of fluoroapatite, anglesite and barite, respectively.

Simultaneous structure refinement of neutron, synchrotron and X-ray powder diffraction patterns

1988 ◽  
Vol 21 (1) ◽  
pp. 22-28 ◽  
Author(s):  
J. K. Maichle ◽  
J. Ihringer ◽  
W. Prandl
Keyword(s):  
Powder Diffraction ◽  
Goodness Of Fit ◽  
Structural Model ◽  
Rietveld Method ◽  
Structure Refinement ◽  
Data Sets ◽  
Data Set ◽  
X Ray ◽  
Counting Statistics ◽  
The Individual

A technique has been developed for the simultaneous analysis of several powder diffraction data on the basis of the Rietveld method. Counting rates from one specimen at a given temperature taken at neutron, synchrotron or X-ray powder diffractometers are joined to one single data set with weights given by the counting statistics. The structure is refined from this data set with a parameter field containing one structural model and individual zero points, scale factors and FWHM parameters for each of the methods and data sets. A new definition of the residuals is given. The residuals and goodness-of-fit values are calculated for all as well as for the individual data sets.

A comparison of a microfocus X-ray source and a conventional sealed tube for crystal structure determination

2009 ◽  
Vol 42 (5) ◽  
pp. 885-891 ◽  
Author(s):  
Thomas Schulz ◽  
Kathrin Meindl ◽  
Dirk Leusser ◽  
Daniel Stern ◽  
Jürgen Graf ◽  
...  
Keyword(s):  
Cross Section ◽  
Data Sets ◽  
Large Crystal ◽  
X Ray ◽  
Heavy Atoms ◽  
Graphite Monochromator ◽  
Small Crystals ◽  
Ccd Detector ◽  
Beam Characteristics

Experiments are described in which a direct comparison was made between a conventional 2 kW water-cooled sealed-tube X-ray source and a 30 W air-cooled microfocus source with focusing multilayer optics, using the same goniometer, detector, radiation (Mo Kα), crystals and software. The beam characteristics of the two sources were analyzed and the quality of the resulting data sets compared. The Incoatec Microfocus Source (IµS) gave a narrow approximately Gaussian-shaped primary beam profile, whereas the Bruker AXS sealed-tube source, equipped with a graphite monochromator and a monocapillary collimator, had a broader beam with an approximate intensity plateau. Both sources were mounted on the same Bruker D8 goniometer with a SMART APEX II CCD detector and Bruker Kryoflex low-temperature device. Switching between sources simply required changing the software zero setting of the 2θ circle and could be performed in a few minutes, so it was possible to use the same crystal for both sources without changing its temperature or orientation. A representative cross section of compounds (organic, organometallic and salt) with and without heavy atoms was investigated. For each compound, two data sets, one from a small and one from a large crystal, were collected using each source. In another experiment, the data quality was compared for crystals of the same compound that had been chosen so that they had dimensions similar to the width of the beam. The data were processed and the structures refined using standard Bruker andSHELXsoftware. The experiments show that the IµS gives superior data for small crystals whereas the diffracted intensities were comparable for the large crystals. Appropriate scaling is particularly important for the IµS data.

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