Determination of the Apparent Crystal Structure of a Highly Faulted UPRM-5 Type Flexible Porous Titanium Silicate via a Polymorph Based Superposition Model, a Rietveld Refinement and a Pair Distribution Function

2014 ◽  
Vol 118 (17) ◽  
pp. 8859-8867 ◽  
Author(s):  
José N. Primera-Pedrozo ◽  
Sneha Dugar ◽  
María M. Martínez-Iñesta ◽  
Riqiang Fu ◽  
Arturo J. Hernández-Maldonado
Keyword(s):  
Crystal Structure ◽  
Distribution Function ◽  
Rietveld Refinement ◽  
Pair Distribution Function ◽  
Porous Titanium ◽  
Superposition Model ◽  
Titanium Silicate

scholarly journals Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing

2021 ◽  
Vol 54 (3) ◽  
Author(s):  
Carina Schlesinger ◽  
Stefan Habermehl ◽  
Dragica Prill
Keyword(s):  
Crystal Structure ◽  
Distribution Function ◽  
Organic Compounds ◽  
Structure Determination ◽  
Local Structure ◽  
Pair Distribution Function ◽  
Barbituric Acid ◽  
Structure Solution ◽  
Global Fit

A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called `PDF-Global-Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data.

scholarly journals Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses

Minerals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 272
Author(s):  
Seungyeol Lee ◽  
Huifang Xu ◽  
Hongwu Xu ◽  
Joerg Neuefeind
Keyword(s):  
Crystal Structure ◽  
Distribution Function ◽  
Single Crystal ◽  
Pair Distribution Function ◽  
Atomic Displacement ◽  
Single Crystal Xrd ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutron Pair ◽  
Atomic Displacement Parameters

The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.

scholarly journals Structure determination of molecular nanocomposites by combining pair distribution function analysis and solid-state NMR

RSC Advances ◽  
2015 ◽  
Vol 5 (12) ◽  
pp. 8895-8902 ◽  
Author(s):  
E.-E. Bendeif ◽  
A. Gansmuller ◽  
K.-Y. Hsieh ◽  
S. Pillet ◽  
Th. Woike ◽  
...  
Keyword(s):  
Distribution Function ◽  
Solid State ◽  
Solid State Nmr ◽  
Pair Distribution Function ◽  
Function Analysis ◽  
Structural Characterisation ◽  
Atomic Pair Distribution Function ◽  
X Ray Scattering ◽  
Atomic Pair

Total X-ray scattering coupled to atomic pair distribution function analysis (PDF) and solid state NMR allowed the identification and structural characterisation of isolated molecules and nanocrystals of sodium nitroprusside confined in mesoporous silica.

The use of restraints in Rietveld refinement of molecular compounds; a case study using the crystal structure determination of tryptamine free base

2002 ◽  
Vol 58 (5) ◽  
pp. 835-840 ◽  
Author(s):  
Harriott Nowell ◽  
J. Paul Attfield ◽  
Jason C. Cole
Keyword(s):  
Crystal Structure ◽  
Rietveld Refinement ◽  
Free Base ◽  
Final Choice ◽  
X Ray ◽  
Global Weight ◽  
Efficient Packing ◽  
Molecular Compounds

The previously unknown crystal structure of the biogenic compound tryptamine, in the form of a free base (C10H12N2), has been solved from X-ray powder diffraction data using simulated annealing followed by restrained Rietveld refinement [space group P212121, a = 12.28593 (6), b = 8.53351 (4), c = 8.49385 (4) Å, Z = 4, final reduced-χ2 = 5.255]. A restrained Rietveld refinement was carried out in which the global weight factor, f, of the stereochemical restraints was gradually lowered. The effect of the relaxation of restraints on the crystal structure and on χ2 was studied and a criterion for the final choice of f is reported. The crystal structure reported here shows efficient packing involving weak intermolecular hydrogen bonding and a herringbone-type packing pattern.

scholarly journals A simple correction for the parallax effect in X-ray pair distribution function measurements

2019 ◽  
Vol 52 (5) ◽  
pp. 1072-1076 ◽  
Author(s):  
Frederick Marlton ◽  
Oleh Ivashko ◽  
Martin v. Zimmerman ◽  
Olof Gutowski ◽  
Ann-Christin Dippel ◽  
...  
Keyword(s):  
Distribution Function ◽  
Rietveld Refinement ◽  
Powder Diffraction ◽  
Pair Distribution Function ◽  
Reference Data ◽  
Real Space ◽  
X Ray ◽  
Local Structures ◽  
Pdf Analysis ◽  
Complex Nanostructures

Total scattering and pair distribution function (PDF) analysis has created new insights that traditional powder diffraction methods have been unable to achieve in understanding the local structures of materials exhibiting disorder or complex nanostructures. Care must be taken in such analyses as subtle and discrete features in the PDF can easily be artefacts generated in the measurement process, which can result in unphysical models and interpretation. The focus of this study is an artefact called the parallax effect, which can occur in area detectors with thick detection layers during the collection of X-ray PDF data. This effect results in high-Q peak offsets, which subsequently cause an r-dependent shift in the PDF peak positions in real space. Such effects should be accounted for if a truly accurate model is to be achieved, and a simple correction that can be conducted via a Rietveld refinement against the reference data is proposed.

scholarly journals Total-scattering pair-distribution function analysis of zinc from high-energy synchrotron data

2019 ◽  
Vol 33 (33) ◽  
pp. 1950410 ◽  
Author(s):  
Ahmad S. Masadeh ◽  
Moneeb T. M. Shatnawi ◽  
Ghosoun Adawi ◽  
Yang Ren
Keyword(s):  
Crystal Structure ◽  
Distribution Function ◽  
Pair Distribution Function ◽  
Function Analysis ◽  
High Energy ◽  
Ambient Conditions ◽  
Total Scattering ◽  
X Ray ◽  
Zinc Metal ◽  
Pdf Analysis

The crystal structure of zinc metal deviates from the ideal hexagonal close packing structure by a significantly increased axial ratio (c/a). The local atomic structure of zinc metal is investigated using the total scattering atomic pair distribution function (PDF) analysis based on X-ray powder diffraction data collected at ambient conditions. The X-ray total scattering PDF analysis confirms that the crystal structure of zinc can be described in terms of wurtzite structure, but with an anomalously atomic displacement parameters [Formula: see text], indicating a significant displacement disorder along the [Formula: see text]-axis. For the long [Formula: see text]-range PDF refinements, the thermal motion of zinc shows a notable anisotropy as expressed by the ratio [Formula: see text]/[Formula: see text] of 2.5 at ambient conditions. This average distortion level along the [Formula: see text]-axis, was not reflected locally for the features below 5.0 Å as it fits the high [Formula: see text] region. Based on PDF refinements over different [Formula: see text]-ranges, we measure an interesting increase of the [Formula: see text] value with decreasing the [Formula: see text]-range of the refinement. This suggests that the local structure features in zinc metal differ from the average structure ones.

scholarly journals Structure determination of molecular nanocomposites by combining pair distribution function analysis and solid-state NMR

2015 ◽  
Vol 71 (a1) ◽  
pp. s383-s384
Author(s):  
Dominik Schaniel ◽  
El-Eulmi Bendeif ◽  
Axel Gansmuller ◽  
Kuan-Ying Hsieh ◽  
Sebastien Pillet ◽  
...  
Keyword(s):  
Distribution Function ◽  
Solid State ◽  
Structure Determination ◽  
Solid State Nmr ◽  
Pair Distribution Function ◽  
Function Analysis
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