scholarly journals Evaluating structures derived from X-ray powder diffraction data using entropy

2014 ◽  
Vol 70 (a1) ◽  
pp. C104-C104
Author(s):  
Dubravka Sisak Jung ◽  
Lynne McCusker ◽  
Christian Baerlocher ◽  
Christopher Gilmore
Keyword(s):  
Powder Diffraction ◽  
Evaluation Criteria ◽  
Entropy Method ◽  
Basis Set ◽  
Solution Quality ◽  
Powder Charge ◽  
X Ray ◽  
Density Maps ◽  
Straightforward Method ◽  
All Solutions

So far, in the field of X-ray powder diffraction, the maximum entropy method (MEM) has been used to (i) solve the phase problem, (ii) estimate the intensities of overlapping reflections, (iii) predict the intensities of missing reflections, and (iv) improve electron density maps generated during Rietveld refinement. We found a new application for MEM in a recent study, in which the powder charge flipping algorithm [1] in Superflip was applied to all-light-atom structures [2]. It proved to be difficult to identify the few fully interpretable maps within in the 200 generated in a typical Superflip job using the standard evaluation criteria. In 1992, Sato reported that entropy could be used as a solution evaluation criterion if the basis set is large, the phases are close to the correct ones, and the structure contains a small molecule [3]. Reasoning that these requirements would be fulfilled by the better Superflip solutions, all solutions were input to the MEM program MICE to calculate the corresponding ME maps and their entropies. Tests performed on several datasets showed no direct correlation between entropy and the solution quality. However, it was noted that a certain number of solutions show entropy values significantly lower than the others. This group usually contained one fully interpretable map. Refinement of the approach led to a relatively straightforward method for recognizing the better solutions. Furthermore, phase recycling based on this approach proved to be useful. As a result, guidelines for solving structures of different levels of complexity using the pCF algorithm could be devised.

Element-selective charge density visualization of endohedral metallofullerenes using synchrotron X-ray multi-wavelength anomalous powder diffraction data

2013 ◽  
Vol 46 (3) ◽  
pp. 649-655 ◽  
Author(s):  
Sachiko Maki ◽  
Eiji Nishibori ◽  
Daisuke Kawaguchi ◽  
Makoto Sakata ◽  
Masaki Takata ◽  
...  
Keyword(s):  
Charge Density ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Rietveld Analysis ◽  
Entropy Method ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Density Maps ◽  
Medium Resolution ◽  
Multi Wavelength

An algorithm for determining the element-selective charge density has been developed using the maximum entropy method (MEM), Rietveld analysis and synchrotron X-ray multi-wavelength anomalous powder diffraction data. This article describes in detail both experimental and analytical aspects of the developed method. A structural study of yttrium mono-metallofullerene, Y@C82, 1:1 co-crystallized with toluene using the present technique is reported in order to demonstrate the applicability of the method even when only medium resolution data are available (d> 1.32 Å). Element-selective MEM charge density maps, computed from synchrotron X-ray powder diffraction data collected at three distinct wavelengths around the yttriumK-absorption edge (∼0.727 A), are employed for determining three crystallographic sites of the disordered yttrium.

Transient electron density maps from femtosecond x-ray powder diffraction

2014 ◽  
Vol 70 (a1) ◽  
pp. C100-C100
Author(s):  
Vincent Juvé ◽  
Flavio Zamponi ◽  
Marcel Holtz ◽  
Michael Woerner ◽  
Thomas Elsaesser
Keyword(s):  
Charge Transfer ◽  
Electron Density ◽  
Powder Diffraction ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
X Rays ◽  
X Ray ◽  
Density Maps ◽  
Structure Factors ◽  
Diffraction Angle

Ultrashort hard x-ray pulses are sensitive probes of structural dynamics on the picometer length and femtosecond time scales of electronic and atomic motions. Using short hard x-ray pulses as probe in a pump-probe scheme allow to do femtosecond x-ray diffraction experiments [1], which provide transient electron density maps at a femtosecond timescale with a sub-angstrom spatial resolution. In a typical femtosecond x-ray powder diffraction experiment many Debye-Scherrer rings, up to a maximum diffraction angle 2θmax, are recorded for each time delay between the optical pump and the hard x-ray probe. From the diffraction pattern, the change of the diffracted intensity of each rings are monitored. The interference of diffracted x-rays from the many unexcited cells, with known structure factors coming from steady-state measurement, and diffracted x-rays from the few excited cells allows for the detection of the transients structure factors. Problems could arise if the 3D-Fourier transform is directly used because of the abrupt end of the collected information in the reciprocal space (maximum diffraction angle 2θmax). In order to overcome this problem, the Maximum Entropy Method is apply to the data and the transient electron density maps are derived. We apply the femtosecond x-ray powder diffraction technique and the Maximum Entropy Method to study the induced transient polarization by high optical fields on ionic crystals. Such polarizations are connected to a spatial redistribution of electronic charge, which corresponds to a charge transfer between the two ionic compounds [2]. While the charge transfer originates from the anion to the cation in the LiBH and the NaBH4, the LiH exhibits a peculiar behavior: the charge transfer occurs from the cation to the anion. As result from comparison with calculations in the COHSEX framework, this behavior is due to the strong electronic correlations in the LiH [3].

Using phases retrieved from two-dimensional projections to facilitate structure solution from X-ray powder diffraction data

2011 ◽  
Vol 44 (5) ◽  
pp. 1023-1032 ◽  
Author(s):  
Dan Xie ◽  
Christian Baerlocher ◽  
Lynne B. McCusker
Keyword(s):  
Electron Microscopy ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Two Dimensional ◽  
Powder Diffraction Data ◽  
Phase Information ◽  
Powder Charge ◽  
X Ray ◽  
Structure Solution ◽  
Using Data

A single-crystal charge-flipping algorithm has been applied to two-dimensional projections derived from X-ray powder diffraction data to retrieve structure-factor phases. These phases proved to be as reliable as those obtained from high-resolution transmission electron microscopy (HRTEM) images or from precession electron diffraction data. In particular, the stronger reflections tend to be correctly phased. The two-dimensional electron-density `images' obtained in this way show the same features as the corresponding HRTEM images, but with higher resolution. Application of the powder charge-flipping algorithm to the full three-dimensional powder diffraction data in conjunction with phases derived from several such (arbitrarily selected) projections was found to have a significant and beneficial effect on the structure solution. The approach was first developed using data collected on the complex zeolite TNU-9, and was then tested further using data for IM-5 and SSZ-74, two similarly complex zeolites. All three of these structures were originally solved by combining X-ray powder diffraction and electron microscopy data, because X-ray diffraction data alone were not sufficient. In all three cases, the phase information derived from two-dimensional subsets of the X-ray powder diffraction data resulted in a significant improvement in the electron-density maps generated by the powder charge-flipping algorithm. The inclusion of this phase information allowed all three structures to be determined from the X-ray data alone. This two-dimensional X-ray powder diffraction approach appears to offer a remarkably simple and powerful method for solving the structures of complex polycrystalline materials.

Charge density studies utilizing powder diffraction and MEM. Exploring of high Tc superconductors, C60 superconductors and manganites

2001 ◽  
Vol 216 (2) ◽  
Author(s):  
M. Takata ◽  
E. Nishibori ◽  
M. Sakata
Keyword(s):  
Charge Density ◽  
Maximum Entropy ◽  
Powder Diffraction ◽  
Recent Progress ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
High Tc Superconductors ◽  
High Tc ◽  
X Ray

AbstractThe recent progress of the accurate charge density studies by the Maximum Entropy Method(MEM) utilizing X-ray powder diffraction is reviewed with some examples. Results for PrBCO (PrBa

Solving complex open-framework structures from X-ray powder diffraction by direct-space methods using composite building units

2013 ◽  
Vol 46 (4) ◽  
pp. 1094-1104 ◽  
Author(s):  
A. Ken Inge ◽  
Henrik Fahlquist ◽  
Tom Willhammar ◽  
Yining Huang ◽  
Lynne B. McCusker ◽  
...  
Keyword(s):  
Ir Spectra ◽  
Powder Diffraction ◽  
Unit Cell ◽  
Complex Case ◽  
Asymmetric Unit ◽  
Powder Charge ◽  
Space Group ◽  
X Ray ◽  
Open Framework ◽  
Structure Solution

The crystal structure of a novel open-framework gallogermanate, SU-66 {|(C6H18N2)18(H2O)32|[Ga4.8Ge87.2O208]}, has been solved from laboratory X-ray powder diffraction (XPD) data by using a direct-space structure solution algorithm and local structural information obtained from infrared (IR) spectroscopy. IR studies on 18 known germanates revealed that the bands in their IR spectra were characteristic of the different composite building units (CBUs) present in the structures. By comparing the bands corresponding to Ge—O vibrations in the IR spectra of SU-66 with those of the 18 known structures with different CBUs, the CBU of SU-66 could be identified empirically as the Ge10(O,OH)27 cluster (Ge10). The unit cell and space group (extinction symbol P--a; a = 14.963, b = 31.593, c = 18.759 Å) were determined initially from the XPD pattern and then confirmed by selected-area electron diffraction. The structure of SU-66 was solved from the XPD data using parallel tempering as implemented in FOX [Favre-Nicolin & Černý (2002). J. Appl. Cryst. 35, 734–743] by assuming P21 ma symmetry and two Ge10 clusters in the asymmetric unit. Rietveld refinement of the resulting structure using synchrotron XPD data showed the framework structure to be correct and the space group to be Pmma. The framework has extra-large (26-ring) one-dimensional channels and a very low framework density of 10.1 Ge/Ga atoms per 1000 Å3. SU-66, with 55 framework atoms in the asymmetric unit, is one of the more complicated framework structures solved from XPD data. Indeed, 98% of the reflections were overlapping in the XPD pattern used for structure solution. Tests on other open-framework germanates (SU-62, SU-65, SU-74, PKU-12 and ITQ-37) for which the XPD data, unit cell, space group and IR spectra were available proved to be equally successful. In a more complex case (SU-72) the combination of FOX and powder charge flipping was required for structure solution.

X-Ray Characterization of Ag Impurities in Na1-xAgxCl

2008 ◽  
Vol 278 ◽  
pp. 33-44 ◽  
Author(s):  
Ramachandran Saravanan ◽  
K.S. Syed Ali ◽  
M. Prema Rani ◽  
R. Saravanan
Keyword(s):  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Entropy Method ◽  
Data Sets ◽  
Density Profiles ◽  
X Ray ◽  
Density Maps ◽  
Electron Density Profiles

The alkali halide Na1-xAgxCl, with two different compositions (x = 0.03 and 0.10), was studied with regard to the Ag impurities in terms of the bonding and electron density distribution. X-ray single crystal data sets have been used for the purpose. The present analysis focused on the electron density distribution and hence the interaction between the atoms is clearly revealed by maximum entropy method (MEM) and multipole analyses. The bonding in these systems has been studied using two-dimensional MEM electron density maps on the (100) and (110) planes and onedimensional electron density profiles along the [100], [110] and [111] directions. The mid-bond electron densities between atoms in these systems are found to be 0.175 e/Å3 and 0.183 e/Å3, respectively, for Na0.97Ag0.03Cl and Na0.90Ag0.10Cl. Multipole analysis of the structure has been performed for these two systems, with respect to the expansion/contraction of the ion involved.

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

2008 ◽  
Vol 41 (6) ◽  
pp. 1115-1121 ◽  
Author(s):  
Dan Xie ◽  
Christian Baerlocher ◽  
Lynne B. McCusker
Keyword(s):  
Electron Diffraction ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Electron Diffraction Data ◽  
Powder Diffraction Data ◽  
Powder Charge ◽  
X Ray ◽  
Structure Solution ◽  
Precession Electron Diffraction ◽  
Using Data

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.

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