Atomic displacement parameters

2013 ◽  
pp. 231-245
Author(s):  
W. F. Kuhs
Keyword(s):  
Atomic Displacement ◽  
Atomic Displacement Parameters

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 Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

2021 ◽  
Vol 8 (4) ◽  
pp. 044701
Author(s):  
Zhen Su ◽  
Medhanjali Dasgupta ◽  
Frédéric Poitevin ◽  
Irimpan I. Mathews ◽  
Henry van den Bedem ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Atomic Displacement ◽  
Potential Utility ◽  
X Ray ◽  
Protein X ◽  
Atomic Displacement Parameters

Incommensurate modulation of calcium barium niobate (CBN28 and Ce:CBN28)

2012 ◽  
Vol 68 (2) ◽  
pp. 101-106 ◽  
Author(s):  
Heribert A. Graetsch ◽  
Chandra Shekhar Pandey ◽  
Jürgen Schreuer ◽  
Manfred Burianek ◽  
Manfred Mühlberg
Keyword(s):  
Crystal Structures ◽  
Tungsten Bronze ◽  
Atomic Displacement ◽  
Type Structure ◽  
Formula Unit ◽  
Tetragonal Tungsten Bronze ◽  
First Order ◽  
Oxygen Coordination ◽  
Incommensurate Modulation ◽  
Atomic Displacement Parameters

The incommensurately modulated crystal structures of Ca0.28Ba0.72Nb2O6 (CBN28) and Ce0.02Ca0.25Ba0.72Nb2O6 (Ce:CBN28) were refined in the supercentred setting X4bm(AA0,−AA0) of the 3 + 2-dimensional superspace group P4bm(aa½,−aa½). Both compounds are isostructural with a tetragonal tungsten bronze-type structure. The modulation of CBN28 consists of a wavy distribution of Ba and Ca atoms as well as vacancies on the incompletely occupied Me2 site with 15-fold oxygen coordination. The occupational modulation is coupled with a modulation of the atomic displacement parameters and a very weak modulation of the positional parameters of Me2. The surrounding O atoms show strong displacive modulations with amplitudes up to ca 0.2 Å owing to the cooperative tilting of the rigid NbO6 octahedra. The Me1 site with 12-fold coordination and Nb atoms are hardly affected by the modulations. Only first-order satellites were observed and the modulations are described by first-order harmonics. In Ce:CBN28 cerium appears to be located on both the Me2 and Me1 sites. Wavevectors and structural modulations are only weakly modified upon substitutional incorporation of 0.02 cerium per formula unit of calcium.

scholarly journals Structural analysis and multipole modelling of quercetin monohydrate – a quantitative and comparative study

2010 ◽  
Vol 67 (1) ◽  
pp. 63-78 ◽  
Author(s):  
Sławomir Domagała ◽  
Parthapratim Munshi ◽  
Maqsood Ahmed ◽  
Benoît Guillot ◽  
Christian Jelsch
Keyword(s):  
Comparative Study ◽  
Charge Density ◽  
Topological Analysis ◽  
Atomic Displacement ◽  
X Ray Diffraction ◽  
Experimental Database ◽  
Figures Of Merit ◽  
Atom Model ◽  
Atomic Displacement Parameters ◽  
Model Approach

The multipolar atom model, constructed by transferring the charge-density parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement parameters, the residual electron densities and the crystallographic figures of merit. The charge-density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately.

scholarly journals Non-metamict betafite from Le Carcarelle (Vico volcanic complex, Italy): occurrence and crystal structure

2004 ◽  
Vol 68 (6) ◽  
pp. 939-950 ◽  
Author(s):  
F. Cámara ◽  
C. T. Williams ◽  
G. Della Ventura ◽  
R. Oberti ◽  
E. Caprilli
Keyword(s):  
Structure Refinement ◽  
Atomic Displacement ◽  
Campi Flegrei ◽  
Volcanic Complex ◽  
Crystal Chemical Formula ◽  
Static Disorder ◽  
Pyrochlore Group ◽  
Atomic Displacement Parameters ◽  
Miarolitic Cavities ◽  
Ti Content

AbstractNon-metamict betafite, a pyrochlore-group mineral with general formula A2−mB2XO6Y(O,OH,F)1−n·pH2O and 2 Ti > Nb+Ta and U > 20% at the A site, has been found at Le Carcarelle, (Latium, Italy). It occurs within miarolitic cavities of a foid-bearing syenitic ejectum enclosed within the pyroclastic formation known as “ignimbrite C”, which belongs to the main effusive phase of the Vico volcanic complex. The host rock is composed of K-feldspar, biotite, augitic clinopyroxene, magnetite and minor sodalite. Electron microprobe analyses gave the following crystal-chemical formula: (Ca1.24Na0.17U0.49REE0.03)Σ=1.93 (Ti1.05Nb0.76Zr0.14Fe0.04Ta0.01)Σ=2.00O6(O,OH). Compared with other occurrences reported in the mineralogical literature, betafite from Le Carcarelle is extremely enriched in U and depleted in Th. Due to its young age of formation (∼150 k.y.), this betafite sample is highly crystalline, thus allowing structure refinement of unheated material. Betafite from Le Carcarelle is cubic Fd3̅m, with a = 10.2637(13) Å, and V = 1081.21(35) Å3, and has a smaller A site (consistent with the higher U content), and a larger and more distorted B site (consistent with the higher Ti content) than calciobetafite from Campi Flegrei, Italy (Mazzi and Munno, 1983). Analysis of the atomic displacement parameters provides evidence for static disorder at the X site.

Neutron powder diffraction studies as a function of temperature of structure II hydrate formed from propane

2003 ◽  
Vol 81 (1-2) ◽  
pp. 431-438 ◽  
Author(s):  
C J Rawn ◽  
A J Rondinone ◽  
B C Chakoumakos ◽  
S Circone ◽  
L A Stern ◽  
...  
Keyword(s):  
Powder Diffraction ◽  
Structure Type ◽  
Atomic Displacement ◽  
Host Lattice ◽  
Neutron Powder Diffraction ◽  
Lattice Data ◽  
Structural Refinement ◽  
Neutron Powder Diffraction Data ◽  
Atomic Displacement Parameters ◽  
Atomic Coordinates

Neutron powder diffraction data confirm that hydrate samples synthesized with propane crystallize as structure type II hydrate. The structure has been modeled using rigid-body constraints to describe C3H8 molecules located in the eight larger polyhedral cavities of a deuterated host lattice. Data were collected at 12, 40, 100, 130, 160, 190, 220, and 250 K and used to calculate the thermal expansivity from the temperature dependence of the lattice parameters. The data collected allowed for full structural refinement of atomic coordinates and the atomic-displacement parameters. PACS No.: 61.12-q

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