scholarly journals Electronic Excitations and Radiation Damage in Macromolecular Crystallography

Crystals ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 273 ◽  
Author(s):  
José Brandão-Neto ◽  
Leonardo Bernasconi
Keyword(s):  
Chemical Information ◽  
X Rays ◽  
Electronic Excitations ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Structures ◽  
Successful Approach ◽  
Structural Research

Macromolecular crystallography at cryogenic temperatures has so far provided the majority of the experimental evidence that underpins the determination of the atomic structures of proteins and other biomolecular assemblies by means of single crystal X-ray diffraction experiments. One of the core limitations of the current methods is that crystal samples degrade as they are subject to X-rays, and two broad groups of effects are observed: global and specific damage. While the currently successful approach is to operate outside the range where global damage is observed, specific damage is not well understood and may lead to poor interpretation of the chemistry and biology of the system under study. In this work, we present a phenomenological model in which specific damage is understood as the result of a single process, the steady excitation of crystal electrons caused by X-ray absorption, which acts as a trigger for the bulk effects that manifest themselves in the form of global damage and obscure the interpretation of chemical information from XFEL and synchrotron structural research.

scholarly journals Electronic Excitations and Radiation Damage in Macromolecular Crystallography

2018 ◽  
Author(s):  
José Brandão-Neto ◽  
Leonardo Bernasconi
Keyword(s):  
Chemical Information ◽  
X Rays ◽  
Electronic Excitations ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Structures ◽  
Successful Approach ◽  
Structural Research

Macromolecular crystallography at cryogenic temperatures has so far provided the majority of the experimental evidence that underpins the determination of the atomic structures of proteins and other biomolecular assemblies by means of single crystal X-ray diffraction experiments. One of the core limitations of the current methods is that crystal samples degrade as they are subject to X-rays, and two broad groups of effects are observed: global and specific damage. While the currently successful approach is to operate outside the range where global damage is observed, specific damage is not well understood and may lead to poor interpretation of the chemistry and biology of the system under study. In this work, we present a phenomenological model in which specific damage is understood as the result of a single process, the steady excitation of crystal electrons caused by X-ray absorption, which acts as a trigger for the bulk effects that manifest themselves in the form of global damage and obscure the interpretation of chemical information from XFEL and synchrotron structural research.

scholarly journals Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources

2019 ◽  
Vol 20 (6) ◽  
pp. 1401 ◽  
Author(s):  
Marius Schmidt
Keyword(s):  
Structural Biology ◽  
Free Electron ◽  
Reaction Dynamics ◽  
X Rays ◽  
Free Electron Lasers ◽  
Macromolecular Crystallography ◽  
Time Resolved ◽  
X Ray ◽  
Methodological Aspects

The focus of structural biology is shifting from the determination of static structures to the investigation of dynamical aspects of macromolecular function. With time-resolved macromolecular crystallography (TRX), intermediates that form and decay during the macromolecular reaction can be investigated, as well as their reaction dynamics. Time-resolved crystallographic methods were initially developed at synchrotrons. However, about a decade ago, extremely brilliant, femtosecond-pulsed X-ray sources, the free electron lasers for hard X-rays, became available to a wider community. TRX is now possible with femtosecond temporal resolution. This review provides an overview of methodological aspects of TRX, and at the same time, aims to outline the frontiers of this method at modern pulsed X-ray sources.

scholarly journals Macromolecular crystallography using neutrons

2014 ◽  
Vol 36 (3) ◽  
pp. 40-42
Author(s):  
Matthew Blakeley
Keyword(s):  
Nucleic Acids ◽  
Biological Systems ◽  
Biological Macromolecules ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Vast Array ◽  
X Ray ◽  
Macromolecular Assemblies

When you think about macromolecular crystallography, the technique that most often comes to mind is X-ray diffraction and it's no wonder. Over 88000 structures of biological macromolecules – from proteins and nucleic acids to viruses and macromolecular assemblies – have been determined using X-rays, and these have contributed significantly to our understanding of a vast array of biological systems and processes.

The Measurement of Elastic Constants for the Determination of Stresses by X-Rays

1983 ◽  
Vol 27 ◽  
pp. 159-170 ◽  
Author(s):  
K. Perry ◽  
I.C. Noyan ◽  
P.J. Rudnik ◽  
J.B. Cohen
Keyword(s):  
Interplanar Spacing ◽  
Measuring System ◽  
Laboratory System ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Measured Change ◽  
Non Destructive ◽  
Applied Stresses

Residual and applied stresses (σij) are often measured via X-ray diffraction, by calculating the resultant elastic strains (ϵij) from the measured change in interplanar spacing (“d”). This method is non-destructive, reasonably reproducible (typically ±14 MPa), can be carried out in the field, and is readily automated to give values to an operator-specified precision , Let Li represent the axes of the measuring system with L3 normal to the diffracting planes, and Pi represent the sample axes. These axes are illustrated in Figure 1. In what follows, primed stresses and strains are in the laboratory system, while unprimed values are in the sample system.

scholarly journals DLSR: a solution to the parallax artefact in X-ray diffraction computed tomography data

2020 ◽  
Vol 53 (6) ◽  
pp. 1531-1541
Author(s):  
A. Vamvakeros ◽  
A. A. Coelho ◽  
D. Matras ◽  
H. Dong ◽  
Y. Odarchenko ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Tomographic Reconstruction ◽  
Scale Up ◽  
Lattice Parameter ◽  
Chemical Information ◽  
X Rays ◽  
X Ray Diffraction ◽  
Major Barrier ◽  
X Ray ◽  
Tomography Data

A new tomographic reconstruction algorithm is presented, termed direct least-squares reconstruction (DLSR), which solves the well known parallax problem in X-ray-scattering-based experiments. The parallax artefact arises from relatively large samples where X-rays, scattered from a scattering angle 2θ, arrive at multiple detector elements. This phenomenon leads to loss of physico-chemical information associated with diffraction peak shape and position (i.e. altering the calculated crystallite size and lattice parameter values, respectively) and is currently the major barrier to investigating samples and devices at the centimetre level (scale-up problem). The accuracy of the DLSR algorithm has been tested against simulated and experimental X-ray diffraction computed tomography data using the TOPAS software.

scholarly journals Determination of structural chirality of berlinite and quartz using resonant x-ray diffraction with circularly polarized x-rays

2010 ◽  
Vol 81 (14) ◽  
Author(s):  
Yoshikazu Tanaka ◽  
Taro Kojima ◽  
Yasutaka Takata ◽  
Ashish Chainani ◽  
Stephen W. Lovesey ◽  
...  
Keyword(s):  
X Rays ◽  
X Ray Diffraction ◽  
Circularly Polarized ◽  
X Ray

scholarly journals Multiple scattering in grazing-incidence X-ray diffraction: impact on lattice-constant determination in thin films

2016 ◽  
Vol 23 (3) ◽  
pp. 729-734 ◽  
Author(s):  
Roland Resel ◽  
Markus Bainschab ◽  
Alexander Pichler ◽  
Theo Dingemans ◽  
Clemens Simbrunner ◽  
...  
Keyword(s):  
Thin Films ◽  
Critical Angle ◽  
Grazing Incidence ◽  
X Rays ◽  
Organic Thin Film ◽  
X Ray Diffraction ◽  
Reliable Determination ◽  
X Ray ◽  
Out Of Plane

Dynamical scattering effects are observed in grazing-incidence X-ray diffraction experiments using an organic thin film of 2,2′:6′,2′′-ternaphthalene grown on oxidized silicon as substrate. Here, a splitting of all Bragg peaks in the out-of-plane direction (z-direction) has been observed, the magnitude of which depends both on the incidence angle of the primary beam and the out-of-plane angle of the scattered beam. The incident angle was varied between 0.09° and 0.25° for synchrotron radiation of 10.5 keV. This study reveals comparable intensities of the split peaks with a maximum for incidence angles close to the critical angle of total external reflection of the substrate. This observation is rationalized by two different scattering pathways resulting in diffraction peaks at different positions at the detector. In order to minimize the splitting, the data suggest either using incident angles well below the critical angle of total reflection or angles well above, which sufficiently attenuates the contributions from the second scattering path. This study highlights that the refraction of X-rays in (organic) thin films has to be corrected accordingly to allow for the determination of peak positions with sufficient accuracy. Based thereon, a reliable determination of the lattice constants becomes feasible, which is required for crystallographic structure solutions from thin films.

Oxford HEXameter: Laboratory High Energy X-Ray Diffractometer for Bulk Residual Stress Analysis

2006 ◽  
Vol 524-525 ◽  
pp. 743-748 ◽  
Author(s):  
Alexander M. Korsunsky ◽  
Shu Yan Zhang ◽  
Daniele Dini ◽  
Willem J.J. Vorster ◽  
Jian Liu
Keyword(s):  
Accurate Determination ◽  
High Energy ◽  
Energy Dispersive ◽  
Detector Response ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
New Instrument ◽  
Synchrotron Beamlines

Diffraction of penetrating radiation such as neutrons or high energy X-rays provides a powerful non-destructive method for the evaluation of residual stresses in engineering components. In particular, strain scanning using synchrotron energy-dispersive X-ray diffraction has been shown to offer a fast and highly spatially resolving measurement technique. Synchrotron beamlines provide best available instruments in terms of flux and low beam divergence, and hence spatial and measurement resolution and data collection rate. However, despite the rapidly growing number of facilities becoming available in Europe and across the world, access to synchrotron beamlines for routine industrial and research use remains regulated, comparatively slow and expensive. A laboratory high energy X-ray diffractometer for bulk residual strain evaluation (HEXameter) has been developed and built at Oxford University. It uses a twin-detector setup first proposed by one of the authors in the energy dispersive X-ray diffraction mode and allows simultaneous determination of macroscopic and microscopic strains in two mutually orthogonal directions that lie approximately within the plane normal to the incident beam. A careful procedure for detector response calibration is used in order to facilitate accurate determination of lattice parameters by pattern refinement. The results of HEXameter measurements are compared with synchrotron X-ray data for several samples e.g. made from a titanium alloy and a particulate composite with an aluminium alloy matrix. Experimental results are found to be consistent with synchrotron measurements and strain resolution close to 2×10-4 is routinely achieved by the new instrument.

X-Ray Diffraction Determination of Texture and Stress in Damascene Fabricated Copper Interconnects

1999 ◽  
Vol 563 ◽  
Author(s):  
Delrose Winter ◽  
Paul R. Besser
Keyword(s):  
Incident Beam ◽  
Preferred Orientation ◽  
Copper Interconnects ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Determination ◽  
Lattice Planes ◽  
Excellent Tool

AbstractX-Ray diffraction (XRD) provides an excellent tool for the measurement of both stress and texture (preferred orientation) on fabricated damascene interconnect structures. Since x-ray diffraction provides a direct measurement of lattice spacings, film strain can be measured directly. Also, since the intensity of diffracted x-rays is proportional to the density of lattice planes oriented in diffracting condition with respect to the incident beam, both the direction and extent of preferred orientation can be accurately measured. Special techniques and considerations are necessary when examining damascene interconnect structures with XRD which are not necessary with blanket films. These techniques are discussed and described in order to aid in obtaining meaningful XRD data and a correct interpretation of the results.

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