scholarly journals Yes, one can obtain better quality structures from routine X-ray data collection

IUCrJ ◽  
2016 ◽  
Vol 3 (1) ◽  
pp. 61-70 ◽  
Author(s):  
W. Fabiola Sanjuan-Szklarz ◽  
Anna A. Hoser ◽  
Matthias Gutmann ◽  
Anders Østergaard Madsen ◽  
Krzysztof Woźniak
Keyword(s):  
Structural Parameters ◽  
Critical Discussion ◽  
Thermal Parameters ◽  
Geometrical Parameters ◽  
Vibrational Entropy ◽  
Structural Investigations ◽  
High Resolution Data ◽  
X Ray ◽  
Atom Model ◽  
Using Data

Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax > 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ < 0.75 Å−1). The TAAM approach is a very good option to obtain more adequate results even using data collected to the lower 2θmax angles. Also the results of translation–libration–screw (TLS) analysis and vibrational entropy values are more reliable for 2θmax > 65°.

New Structural Investigations in the Cu2Se(S)-In2Se3(S)/Cu2Se(S)-Ga2Se3(S) Phase Diagrams

2009 ◽  
Vol 1165 ◽  
Author(s):  
Christiane Stephan ◽  
Susan Schorr ◽  
H.W. Schock
Keyword(s):  
Phase Diagrams ◽  
Structural Parameters ◽  
Homogeneity Region ◽  
Homogeneous Microstructure ◽  
Structural Investigations ◽  
X Ray ◽  
Cu Content ◽  
Α Phase ◽  
Powder Samples ◽  
Trivalent Cations

AbstractNon-stoichiometry is a characteristic feature of ternary chalcopyrites like Cu-III-VI2 (III=In,Ga; VI=S,Se). The results of a comparative study of structural trends within the homogeneity region of the chalcopyrite type α-phase of the Cu2Se(S)-In2Se3(S) and Cu2Se(S)-Ga2Se3(S) quasibinary phase diagrams are presented. Powder samples of Cu-rich and Cu-poor [Cu2Se(S)]1-y-[In2Se3(S)]y as well as [Cu2Se(S)]1-y-[Ga2Se3(S)]y alloys were prepared (0.4<y<0.6) by solid state reaction of the elements (T=850°C) and investigated by X-ray powder diffraction and electron microprobe analysis. It was shown that the grain size depends on composition and structural parameters. The tetragonal distortion η=c/2a has been determined for the different trivalent cations and influences the microstructure in Cu-poor Cu1-xIII1+x/3VI2 samples. In Cu-rich samples the Cu-content is in all cases the driving force for the formation of the homogeneous microstructure observed.

Atomic displacement parameters for Ni(ND3)4(NO2)2 from 9 K X-ray and 13 K time-of-flight neutron diffraction data

1996 ◽  
Vol 52 (6) ◽  
pp. 923-931 ◽  
Author(s):  
B. B. Iversen ◽  
F. K. Larsen ◽  
B. N. Figgis ◽  
P. A. Reynolds ◽  
A. J. Schultz
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Structural Information ◽  
Structural Parameters ◽  
Structure Refinement ◽  
Time Of Flight ◽  
Thermal Parameters ◽  
Neutron Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray

Structural parameters derived from 9 1) K X-ray diffraction data and 13 (1) K time-of-flight neutron diffraction data on perdeuterated tetraamminedinitronickel(II), Ni(ND3)4(NO2)2, are compared. It is shown that excellent agreement can be obtained for both positional and thermal parameters derived separately from the two experiments, provided that great care is taken in all steps of the process, including data collection, data reduction, and nuclear and electronic structure refinement. The mean difference in the thermal parameters, <|ΔUij |>, is as low as 0.00034 Å2 and <(ΔUij/σ)2>1/2 = 1.92, showing that, even without any form of scaling between the parameters, the same values can be obtained. This, compared with other such studies, indicates that time-of-flight neutron diffraction data can give structural information of a quality comparable to monochromatic neutron diffraction. The excellent correspondence between the thermal parameters derived separately from X-ray and neutron diffraction data gives confidence in the deconvolution of the thermal motion from the X-ray diffraction data, which is necessary for any study of a static electron density distribution.

scholarly journals Structure of the 30S ribosomal decoding complex at ambient temperature

2018 ◽  
Author(s):  
E. Han Dao ◽  
Frédéric Poitevin ◽  
Raymond G. Sierra ◽  
Cornelius Gati ◽  
Yashas Rao ◽  
...  
Keyword(s):  
Ambient Temperature ◽  
Messenger Rna ◽  
Thermus Thermophilus ◽  
Ribosomal Subunit ◽  
Temperature Structure ◽  
Structural Studies ◽  
High Resolution Data ◽  
X Ray ◽  
Experimental Limitation ◽  
Using Data

ABSTRACTThe ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New lightsources like the X-ray free electron laser (XFEL) have enabled data collection from macromolecular crystals at ambient temperature. Here, we report an X-ray crystal structure of the Thermus thermophilus 30S ribosomal subunit decoding complex to 3.45 Å resolution using data obtained at ambient temperature at the Linac Coherent Light Source (LCLS). We find that this ambient-temperature structure is largely consistent with existing cryogenic-temperature crystal structures, with key residues of the decoding complex exhibiting similar conformations, including adenosine residues 1492 and 1493. Minor variations were observed, namely an alternate conformation of cytosine 1397 near the mRNA channel and the A-site. Our serial crystallography experiment illustrates the amenability of ribosomal microcrystals to routine structural studies at ambient temperature, thus overcoming a long-standing experimental limitation.

Hydrogen ADPs with CuKα data? Invariom and Hirshfeld atom modelling of fluconazole

2014 ◽  
Vol 70 (6) ◽  
pp. 580-583 ◽  
Author(s):  
Claudia M. Orben ◽  
Birger Dittrich
Keyword(s):  
Single Crystal ◽  
Diffraction Data ◽  
Geometrical Parameters ◽  
X Ray Diffraction ◽  
Atom Density ◽  
X Ray ◽  
Figures Of Merit ◽  
Atom Model ◽  
Anisotropic Displacement Parameters

For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with CuKα radiation to a resolution of sin θ/λ of 0.6 Å−1. The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å−1, but requires good low-order data.

scholarly journals Structural investigations of the α12Si–Ge superstructure

2015 ◽  
Vol 48 (1) ◽  
pp. 262-268 ◽  
Author(s):  
Tanja Etzelstorfer ◽  
Mohammad Reza Ahmadpor Monazam ◽  
Stefano Cecchi ◽  
Dominik Kriegner ◽  
Daniel Chrastina ◽  
...  
Keyword(s):  
Structural Parameters ◽  
X Ray Diffraction ◽  
Structural Investigations ◽  
X Ray ◽  
Direct Bandgap ◽  
Superlattice Structure ◽  
Band Structure Calculations ◽  
Nominal Structure ◽  
Structure Calculations

This article reports the X-ray diffraction-based structural characterization of the α12multilayer structure SiGe2Si2Ge2SiGe12[d'Avezac, Luo, Chanier & Zunger (2012).Phys. Rev. Lett.108, 027401], which is predicted to form a direct bandgap material. In particular, structural parameters of the superlattice such as thickness and composition as well as interface properties, are obtained. Moreover, it is found that Ge subsequently segregates into layers. These findings are used as input parameters for band structure calculations. It is shown that the direct bandgap properties depend very sensitively on deviations from the nominal structure, and only almost perfect structures can actually yield a direct bandgap. Photoluminescence emission possibly stemming from the superlattice structure is observed.

Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

1982 ◽  
Vol 40 ◽  
pp. 74-75
Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser
Keyword(s):  
Purple Membrane ◽  
Data Set ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fourier Techniques ◽  
Versus Protein ◽  
The Difference ◽  
Difference Fourier ◽  
Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

Small angle X-ray scattering study of porosity variation in a styrene-divinylbenzene copolymer

1981 ◽  
Vol 46 (7) ◽  
pp. 1675-1681 ◽  
Author(s):  
Josef Baldrian ◽  
Božena N. Kolarz ◽  
Henrik Galina
Keyword(s):  
Small Angle ◽  
Structural Parameters ◽  
Two Phase ◽  
X Ray ◽  
Porosity Variation ◽  
Swelling Agent ◽  
X Ray Scattering ◽  
Styrene Divinylbenzene ◽  
Ray Scattering

Porosity variations induced by swelling agent exchange were studied in a styrene-divinylbenzene copolymer. Standard methods were used in the characterization of copolymer porosity in the dry state and the results were compared with related structural parameters derived from small angle X-ray scattering (SAXS) measurements as developed for the characterization of two-phase systems. The SAXS method was also used for porosity determination in swollen samples. The differences in the porosity of dry samples were found to be an effect of the drying process, while in the swollen state the sample swells and deswells isotropically.

Strukturuntersuchungen an Diaryldichalkogeniden: Die Molekülstrukturen von [2,4,6-(CF3)3C6H2S]2,[2,4,6-Me3C6H2Te]2 und [2-Me2N-4,6-(CF3)2C6H2Te]2 / Structural Investigations of Diaryl Dichalcogenides: The Molecular Structures of [2,4,6-(CF3)3C6H2S]2, [2,4,6-Me3C6H2Te]2 and [2-Me2N-4,6-(CF3)2C6H2Te]2

1992 ◽  
Vol 47 (3) ◽  
pp. 305-309 ◽  
Author(s):  
Anja Edelmann ◽  
Sally Brooker ◽  
Norbert Bertel ◽  
Mathias Noltemeyer ◽  
Herbert W. Roesky ◽  
...  
Keyword(s):  
Molecular Structures ◽  
Monoclinic Space Group ◽  
Crystal Data ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Structural Investigations ◽  
Space Group ◽  
X Ray

Abstract The Molecular Structures of [2,4,6-(CF3)3C6H2S]2 (1) [2,4,6-Me3C6H2Te]2 and [2-Me2N-4,6-(CF3)2C6H2Te]2 (3) have been determined by X-ray diffraction. Crystal data: 1: orthorhombic, space group P212121, Z = 4, a = 822.3(2), b = 1029.2(2), c = 2526.6(5) pm (2343 observed independent reflexions, R = 0.042); 2: orthorhombic, space group Iba 2, Z = 8, a = 1546.5(2), b = 1578.4(2), c = 1483.9(1) pm (2051 observed independent reflexions, R = 0.030); 3: monoclinic, space group P 21/c, Z = 4, a = 1118.7(1), b = 1536.5(2), c = 1492.6(2) pm, β = 98.97(1)° (3033 observed independent reflexions, R = 0.025).

The Effect of Type and Height of Piers on the Seismic Behavior of Reinforced Concrete Bridges

2019 ◽  
Vol 41 ◽  
pp. 79-87 ◽  
Author(s):  
Mohamed Cherif Djemai ◽  
Mahmoud Bensaibi ◽  
Fatma Zohra Halfaya
Keyword(s):  
Reinforced Concrete ◽  
Structural Parameters ◽  
Strong Motion ◽  
Concrete Bridges ◽  
Geometrical Parameters ◽  
Girder Bridges ◽  
Building Research Institute ◽  
Reinforced Concrete Bridges ◽  
Dynamic Analyses ◽  
Strong Motion Database

Bridges are commonly used lifelines; they play an important role in the economic activity of a city or a region and their role can be crucial in a case of a seismic event since they allow the arrival of the first aid. Reinforced concrete (RC) bridges are worldwide used type view their durability, flexibility and economical cost. In fact, their behavior under seismic loading was the aim of various studies. In the present study the effect of two structural parameters i.e. the height and the type of piers of reinforced concrete bridges on seismic response is investigated. For that reason, different multi-span continuous girder bridges models with various geometrical parameters are considered. Then, non-linear dynamic analyses are performed based on two types of piers which are: multiple columns bent and wall piers with varying heights. In this approach, a serie of 40 ground motions records varying from weak to strong events selected from Building Research Institute (BRI) strong motion database are used including uncertainty in the soil and seismic characteristics. Modelling results put most emphasis on the modal periods and responses of the top pier displacements, they show the influence of the considered parameters on the behavior of such structures and their impact on the strength of reinforced concrete bridges.

Hairline breakage detection in X-ray images using data fusion

2017 ◽  
Vol 77 (13) ◽  
pp. 17207-17222 ◽  
Author(s):  
C. Harriet Linda ◽  
G. Wiselin Jiji
Keyword(s):  
Data Fusion ◽  
X Ray ◽  
Using Data
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