scholarly journals Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data

2021 ◽  
Author(s):  
Paul Klar ◽  
Yasar Krysiak ◽  
Hongyi Xu ◽  
Gwladys Steciuk ◽  
Jung Cho ◽  
...  
Keyword(s):  
Structure Refinement ◽  
Reliable Determination ◽  
Dynamical Diffraction ◽  
Fold Reduction ◽  
Continuous Rotation ◽  
Difference Fourier ◽  
Chiral Crystals ◽  
Diffraction Effects ◽  
Absolute Structure

Dynamical diffraction effects are usually considered a nuisance for structure analysis from continuous-rotation 3D electron diffraction (3D ED) data like cRED and MicroED. Here we demonstrate that by accounting for these effects during the structure refinement, significantly improved models can be obtained in terms of accuracy and reliability with up to four-fold reduction of the noise level in difference Fourier maps in comparison to the standard structure determination routines that ignore dynamical diffraction. As dynamical diffraction effects break the inversion symmetry of the diffraction, they allow a quick, easy, and reliable determination of the absolute structure of chiral crystals.

scholarly journals Structure refinement using precession electron diffraction tomography and dynamical diffraction: tests on experimental data

2015 ◽  
Vol 71 (6) ◽  
pp. 740-751 ◽  
Author(s):  
Lukáš Palatinus ◽  
Cinthia Antunes Corrêa ◽  
Gwladys Steciuk ◽  
Damien Jacob ◽  
Pascal Roussel ◽  
...  
Keyword(s):  
Experimental Data ◽  
Electron Diffraction ◽  
Structure Refinement ◽  
Electron Diffraction Data ◽  
Average Error ◽  
Reference Structure ◽  
Reliable Determination ◽  
Dynamical Diffraction ◽  
Precession Electron Diffraction

The recently published method for the structure refinement from three-dimensional precession electron diffraction data using dynamical diffraction theory [Palatinus et al. (2015). Acta Cryst. A71, 235–244] has been applied to a set of experimental data sets from five different samples – Ni2Si, PrVO3, kaolinite, orthopyroxene and mayenite. The data were measured on different instruments and with variable precession angles. For each sample a reliable reference structure was available. A large series of tests revealed that the method provides structure models with an average error in atomic positions typically between 0.01 and 0.02 Å. The obtained structure models are significantly more accurate than models obtained by refinement using kinematical approximation for the calculation of model intensities. The method also allows a reliable determination of site occupancies and determination of absolute structure. Based on the extensive tests, an optimal set of the parameters for the method is proposed.

scholarly journals Why direct and post-refinement determinations of absolute structure may give different results

2016 ◽  
Vol 72 (5) ◽  
pp. 661-683 ◽  
Author(s):  
David John Watkin ◽  
Richard Ian Cooper
Keyword(s):  
Recent Literature ◽  
Structure Refinement ◽  
Direct Determination ◽  
Standard Uncertainty ◽  
Data Sets ◽  
Normal Probability Plot ◽  
Normal Probability ◽  
Structure Determinations ◽  
Absolute Structure

Direct determination of the Flack parameter as part of the structure refinement procedure usually gives different, though similar, values to post-refinement methods. The source of this discrepancy has been probed by analysing a range of data sets taken from the recent literature. Most significantly, it was observed that the directly refined Flack (x) parameter and its standard uncertainty are usually not much influenced by changes in the refinement weighting schemes, but if they are then there are probably problems with the data or model. Post-refinement analyses give Flack parameters strongly influenced by the choice of weights. Weights derived from those used in the main least squares lead to post-refinement estimates of the Flack parameters and their standard uncertainties very similar to those obtained by direct refinement. Weights derived from the variances of the observed structure amplitudes are more appropriate and often yield post-refinement Flack parameters similar to those from direct refinement, but always with lower standard uncertainties. Substantial disagreement between direct and post-refinement determinations are strongly indicative of problems with the data, which may be difficult to identify. Examples drawn from 28 structure determinations are provided showing a range of different underlying problems. It seems likely that post-refinement methods taking into account the slope of the normal probability plot are currently the most robust estimators of absolute structure and should be reported along with the directly refined values.

scholarly journals Light-Atom Structures: Absolute Configuration Determination and Beyond

2014 ◽  
Vol 70 (a1) ◽  
pp. C965-C965
Author(s):  
Jürgen Graf ◽  
Michael Ruf ◽  
Holger Ott ◽  
Bruce Noll ◽  
Séverine Freisz ◽  
...  
Keyword(s):  
Absolute Configuration ◽  
Quality Data ◽  
Liquid Gallium ◽  
Light Atom ◽  
Reliable Determination ◽  
X Ray ◽  
Anomalous Signal ◽  
The Absolute ◽  
Absolute Structure

The determination of the absolute configuration for light-atom structures is central to research in pharmaceuticals and natural-product synthesis [1]. In the absence of elements heavier than silicon, it is often problematic to make a significant assignment of absolute configuration. Traditionally, heavy-atom derivatives were prepared which have a stronger anomalous signal compared to the native compound. However, this is not always feasible. The assignment of the absolute structure of pure organic compounds has become somewhat easier with the advent of high-intensity microfocus sources [2], as the increased flux density improves the anomalous signal through improvements in counting statistics. In order to maximize the anomalous signal, X-ray sources with Cu anodes are usually used for the absolute structure determination. However, these data are usually limited to a maximum resolution of about 0.80 Å. High-brilliance microfocus X-ray sources with Mo targets enable the collection of high quality data beyond 0.40 Å within a reasonable amount of time. This allows not only a more accurate modelling of the electron density by using aspherical scattering factors, but also enables a reliable determination of the absolute structure, despite the significantly lower anomalous signal obtained with Mo Kα radiation. With the recently introduced liquid-Gallium-jet X-ray source unprecedented beam intensities can be achieved [3]. The shorter wavelength of Ga Kα compared to Cu Kα slightly weakens the anomalous signal of a typical light-atom structure. However, due to the shorter wavelength, the highest resolution for the liquid metal-jet source is typically at about 0.70 Å, compared to about 0.80 Å for Cu Kα. Hence, about 50% more unique reflections can be recorded. This clearly improves the structural model and the quality of the Flack parameter. Selected results on the absolute structure and charge density determinations for light-atom structures will be presented.

scholarly journals Crystal structure refinement withSHELXL

2015 ◽  
Vol 71 (1) ◽  
pp. 3-8 ◽  
Author(s):  
George M. Sheldrick
Keyword(s):  
Crystal Structure ◽  
Structure Refinement ◽  
Crystal Structure Refinement ◽  
Disordered Structures ◽  
Reflection Data ◽  
Structure Factors ◽  
Recent Developments ◽  
Information Framework ◽  
Absolute Structure

The improvements in the crystal structure refinement programSHELXLhave been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data andSHELXLinstructions is needed for a complete structure archive; the programSHREDCIFcan be used to extract the .hkl and .ins files required for further refinement withSHELXL. Recent developments inSHELXLfacilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures.SHELXLis available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

A panel of mono- and dinucleotide microsatellite markers is required for reliable determination of the MSI status in colorectal cancer

2001 ◽  
Vol 120 (5) ◽  
pp. A599-A599
Author(s):  
C ARNOLD ◽  
A GOEL ◽  
J CARETHERS ◽  
L WASSERMAN ◽  
C COMPTON ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Microsatellite Markers ◽  
Reliable Determination

Colorimetric Determination of Fluoride in Drinking Groundwater using a Polymeric Zirconium Complex of 5-(2-Carboxyphenylazo)-8-Hydroxyquinoline

2013 ◽  
Vol 12 (7) ◽  
pp. 460-465
Author(s):  
Sameer Amereih ◽  
Zaher Barghouthi ◽  
Lamees Majjiad
Keyword(s):  
Drinking Water ◽  
Detection Limit ◽  
Complex Formation ◽  
Molar Absorptivity ◽  
Colorimetric Determination ◽  
Zirconium Complex ◽  
Reliable Determination ◽  
Percentage Recovery ◽  
Quantitation Limit

A sensitive colorimetric determination of fluoride in drinking water has been developed using a polymeric zirconium complex of 5-(2-Carboxyphenylazo)-8-Hydroxyquinoline as fluoride reagents. The method allowed a reliable determination of fluoride in range of (0.0-1.5) mg L-1. The molar absorptivity of the complex formation is 7695 ± 27 L mol-1 cm-1 at 460 nm. The sensitivity, detection limit, quantitation limit, and percentage recovery for 1.0 mg L-1 fluoride for the proposed method were found to be 0.353 ± 0.013 μg mL-1, 0.1 mg L-1, 0.3 mg L-1, and 101.7 ± 4.1, respectively.

scholarly journals Fast and Sensitive Determination of the Fungicide Carbendazim in Fruit Juices with an Immunosensor Based on White Light Reflectance Spectroscopy

Biosensors ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 153
Author(s):  
Georgios Koukouvinos ◽  
Chrysoula-Evangelia Karachaliou ◽  
Ioannis Raptis ◽  
Panagiota Petrou ◽  
Evangelia Livaniou ◽  
...  
Keyword(s):  
White Light ◽  
Optical Biosensor ◽  
Reflectance Spectroscopy ◽  
Fruit Juices ◽  
Sample Treatment ◽  
Assay Sensitivity ◽  
Reliable Determination ◽  
Light Reflectance ◽  
Sensitive Determination

Carbendazim is a systemic benzimidazole-type fungicide with broad-spectrum activity against fungi that undermine food products safety and quality. Despite its effectiveness, carbendazim constitutes a major environmental pollutant, being hazardous to both humans and animals. Therefore, fast and reliable determination of carbendazim levels in water, soil, and food samples is of high importance for both food industry and public health. Herein, an optical biosensor based on white light reflectance spectroscopy (WLRS) for fast and sensitive determination of carbendazim in fruit juices is presented. The transducer is a Si/SiO2 chip functionalized with a benzimidazole conjugate, and determination is based on a competitive immunoassay format. Thus, for the assay, a mixture of an in-house developed rabbit polyclonal anti-carbendazim antibody with the standards or samples is pumped over the chip, followed by biotinylated secondary antibody and streptavidin. The WLRS platform allows for real-time monitoring of biomolecular interactions carried out onto the Si/SiO2 chip by transforming the shift in the reflected interference spectrum caused by the immunoreaction to effective biomolecular adlayer thickness. The sensor is able to detect 20 ng/mL of carbendazim in fruit juices with high accuracy and precision (intra- and inter-assay CVs ≤ 6.9% and ≤9.4%, respectively) in less than 30 min, applying a simple sample treatment that alleviates any “matrix-effect” on the assay results and a 60 min preincubation step for improving assay sensitivity. Excellent analytical characteristics and short analysis time along with its small size render the proposed WLRS immunosensor ideal for future on-the-spot determination of carbendazim in food and environmental samples.

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