scholarly journals Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data

2014 ◽  
Vol 70 (5) ◽  
pp. 1491-1497 ◽  
Author(s):  
Jimin Wang ◽  
Richard A. Wing
Keyword(s):  
Electron Density ◽  
Diffraction Data ◽  
Heavy Atom ◽  
Uniform Density ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Correlation ◽  
Atomic Models ◽  
Weak Intensity

Overwhelming evidence exists to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps improve the refinement of atomic models by imposing strong constraints on individual and overall temperatureBfactors and thus the quality of crystal structures. Some researchers consider these data to be of little value and opt to discard them during data processing, particularly at medium and low resolution, at which individualBfactors of atomic models cannot be refined. Here, new evidence is provided to show that the inclusion of these data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry (NCS) averaging. Using electron-density correlation coefficients as criteria, the resolution of data has successfully been extended from 3.1 to 2.5 Å resolution with redundancy-independent mergingRfactors from below 100% to about 310%. It is further demonstrated that phase information can be fully extracted from observed amplitudes throughde novoNCS averaging. Averaging starts with uniform density inside double-shelled spherical masks and NCS matrices that are derived from bound heavy-atom clusters at the vertices of cuboctahedrally symmetric protein particles.

scholarly journals Crystallographic features of ammonium fluoroelpasolites: dynamic orientational disorder in crystals of (NH4)3HfF7 and (NH4)3Ti(O2)F5

2017 ◽  
Vol 73 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Anatoly A. Udovenko ◽  
Alexander A. Karabtsov ◽  
Natalia M. Laptash
Keyword(s):  
Single Crystal ◽  
Electron Density ◽  
Diffraction Data ◽  
Central Atom ◽  
X Ray Diffraction ◽  
Dynamic Nature ◽  
Orientational Disorder ◽  
High Quality ◽  
Structural Units ◽  
X Ray

A classical elpasolite-type structure is considered with respect to dynamically disordered ammonium fluoro-(oxofluoro-)metallates. Single-crystal X-ray diffraction data from high quality (NH4)3HfF7 and (NH4)3Ti(O2)F5 samples enabled the refinement of the ligand and cationic positions in the cubic Fm \bar 3 m (Z = 4) structure. Electron-density atomic profiles show that the ligand atoms are distributed in a mixed (split) position instead of 24e. One of the ammonium groups is disordered near 8c so that its central atom (N1) forms a tetrahedron with vertexes in 32f. However, a center of another group (N2) remains in the 4b site, whereas its H atoms (H2) occupy the 96k positions instead of 24e and, together with the H3 atom in the 32f position, they form eight spatial orientations of the ammonium group. It is a common feature of all ammonium fluoroelpasolites with orientational disorder of structural units of a dynamic nature.

Crystal and Molecular Structure of Dithiocyanato(triphenylarsine)mercury(II)

1975 ◽  
Vol 53 (22) ◽  
pp. 3383-3387 ◽  
Author(s):  
Joseph Hubert ◽  
André L. Beauchamp ◽  
Roland Rivest
Keyword(s):  
Molecular Structure ◽  
Least Squares ◽  
Coordination Number ◽  
Diffraction Data ◽  
Crystal And Molecular Structure ◽  
Heavy Atom ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Heavy Atom Method

The crystal and molecular structure of dithiocyanato(triphenylarsine)mercury(II) has been determined from X-ray diffraction data. The crystals are monoclinic, space group P21/c, with a = 10.290(7), b = 21.199(23), c = 10.719(7) Å, β = 112.00(2)°, and Z = 4. The structure has been solved by the heavy-atom method and refined by block-diagonal least-squares calculations. The agreement factor R obtained for 2607 'observed' reflections is 0.030. The crystal consists of single molecules. The 'characteristic' coordination number of mercury is three, with two sulfur and one arsenic atoms at the apexes of a triangle. The nitrogen atoms of the thiocyanate groups are at 2.67 and 2.74 Å from the adjoining mercury atoms and therefore link the different molecules together.

Experimental electron density study of 1,2,4-triazole at 15 K. A comparison with ab initio-calculations

1997 ◽  
Vol 212 (3) ◽  
Author(s):  
P. Fuhrmann ◽  
T. Koritsánszky ◽  
P. Luger
Keyword(s):  
Ab Initio Calculations ◽  
Ab Initio ◽  
Electron Density ◽  
Diffraction Data ◽  
Topological Properties ◽  
X Ray Diffraction ◽  
X Ray ◽  
Experimental Electron Density ◽  
Density Study

AbstractTopological properties and the Laplacian function of the electron density of 1,2,4-triazole have been determined from X-ray diffraction data collected at 15 K. 1,2,4-Triazole, C

Electron-density Fourier maps of an untwinnedYBa2Cu3O6.877single crystal by x-ray-diffraction data

1993 ◽  
Vol 48 (14) ◽  
pp. 10638-10641 ◽  
Author(s):  
J. D. Sullivan ◽  
P. Bordet ◽  
M. Marezio ◽  
K. Takenaka ◽  
S. Uchida
Keyword(s):  
Electron Density ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray

A combined model of electron density and lattice dynamics refined against elastic diffraction data. Thermodynamic properties of crystalline L-alanine

2020 ◽  
Vol 76 (1) ◽  
pp. 32-44 ◽  
Author(s):  
Ioana Sovago ◽  
Anna A. Hoser ◽  
Anders Ø. Madsen
Keyword(s):  
Dft Calculations ◽  
Electron Density ◽  
Normal Mode ◽  
Diffraction Data ◽  
Lattice Dynamics ◽  
Phonon Dispersion ◽  
Form Factors ◽  
X Ray Diffraction ◽  
Crystalline Materials ◽  
X Ray

Thermodynamic stability is an essential property of crystalline materials, and its accurate calculation requires a reliable description of the thermal motion – phonons – in the crystal. Such information can be obtained from periodic density functional theory (DFT) calculations, but these are costly and in some cases insufficiently accurate for molecular crystals. This deficiency is addressed here by refining a lattice-dynamics model, derived from DFT calculations, against accurate high-resolution X-ray diffraction data. For the first time, a normal-mode refinement is combined with the refinement of aspherical atomic form factors, allowing a comprehensive description and physically meaningful deconvolution of thermal motion and static charge density in the crystal. The small and well diffracting L-alanine system was used. Different lattice-dynamics models, with or without phonon dispersion, and derived from different levels of theory, were tested, and models using spherical and aspherical form factors were compared. The refinements indicate that the vibrational information content in the 23 K data is too small to study lattice dynamics, whereas the 123 K data appear to hold information on the acoustic and lowest-frequency optical phonons. These normal-mode models show slightly larger refinement residuals than their counterparts using atomic displacement parameters, and these features are not removed by considering phonon dispersion in the model. The models refined against the 123 K data, regardless of their sophistication, give calculated heat capacities for L-alanine within less than 1 cal mol−1 K−1 of the calorimetric measurements, in the temperature range 10–300 K. The findings show that the normal-mode refinement method can be combined with an elaborate description of the electron density. It appears to be a promising technique for free-energy determination for crystalline materials at the expense of performing a single-crystal elastic X-ray diffraction determination combined with periodic DFT calculations.

XRD Instrument Sensitivity Results from a Round Robin Study

1991 ◽  
Vol 35 (A) ◽  
pp. 333-340 ◽  
Author(s):  
W.N. Schreiner ◽  
R. Jenkins ◽  
P.F. Dismore
Keyword(s):  
Diffraction Data ◽  
Round Robin ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Diffraction Intensity ◽  
Generic Type ◽  
X Ray ◽  
The Past ◽  
Instrument Sensitivity

During the course of the past ten years the International Centre for Diffraction Data has sponsored a number of “Round Robin” tests to evaluate the quality of experimental X-ray diffraction data [1-5]. The latest of this series, called the Instrument Parameter Round Robin, was designed to evaluate, among other things, relative angularly-dependent sensitivity differences between diffractometers. Previous experiments have indicated that even perfectly aligned diffractometers of the same generic type, do not necessarily give the same set of relative intensities. One objective of the round robin was to quantify the magnitude of the experimental differences between data sets, and to demonstrate a means for external calibration of diffractometers, so that digitized diffraction intensity data obtained from different instruments could be directly compared.

scholarly journals Comparison of the Quality of Protein Crystals Grown by CLPC Seeds Method

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 501 ◽  
Author(s):  
Li ◽  
Yan ◽  
Liu ◽  
Wu ◽  
Liu ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
High Quality ◽  
X Ray ◽  
High Quality Protein

We present a systematic quality comparison of protein crystals obtained with and without cross-linked protein crystal (CLPC) seeds. Four proteins were used to conduct the experiments, and the results showed that crystals obtained in the presence of CLPC seeds exhibited a better morphology. In addition, the X-ray diffraction data showed that the CLPC seeds method is a powerful tool to obtain high-quality protein crystals. Therefore, we recommend the use of CLPC seeds in preparing high-quality diffracting protein crystals.

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