scholarly journals Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography

2019 ◽  
Vol 377 (2145) ◽  
pp. 20170474 ◽  
Author(s):  
Christopher D. M. Hutchison ◽  
Jasper J. van Thor
Keyword(s):  
Structural Dynamics ◽  
Time Domain ◽  
Optical Pumping ◽  
High Repetition Rate ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Vibrational Coherence ◽  
X Ray Crystallography ◽  
Ultrafast Optical

Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays’.

scholarly journals William Lawrence Bragg, 31 March 1890 - 1 July 1971

1979 ◽  
Vol 25 ◽  
pp. 74-143 ◽  
Keyword(s):  
Living Cell ◽  
Inorganic Compounds ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Intensive Work ◽  
Unique Part

Walking along the Backs in Cambridge one day in the autumn of 1912 William Lawrence Bragg had an idea that led immediately to a dramatic advance in physics and has since transformed chemistry, mineralogy, metallurgy and, most recently, biology. He realized that the observations of X-ray diffraction by a crystal, which had been reported by von Laue and his associates earlier in that year, can be interpreted very simply as arising from reflexion of the X-rays by planes of atoms in the crystal and hence that the X-ray observations provide evidence from which the arrangement of atoms in the crystal may be determined. A few weeks of intensive work on simple inorganic compounds were enough to demonstrate the correctness of these ideas but the development of the method, at first in association with his father and later as the leader or guiding influence of a host of workers, was the labour of a lifetime. When he died on 1 July 1971, X-ray crystallography had revealed the arrangement of atoms in matter of all kinds from the simplest of salts to the macromolecules of the living cell. The story of his life is very largely the story of that achievement and the circumstances that led to his unique part in it.

Frontier methods in coherent X-ray diffraction for high-resolution structure determination

2016 ◽  
Vol 49 ◽  
Author(s):  
Marcus Gallagher-Jones ◽  
Jose A. Rodriguez ◽  
Jianwei Miao
Keyword(s):  
Structure Determination ◽  
X Rays ◽  
X Ray Diffraction ◽  
Diffractive Imaging ◽  
X Ray ◽  
Coherent Diffractive Imaging ◽  
X Ray Crystallography ◽  
Max Von Laue ◽  
Complex Protein ◽  
High Resolution Structure

AbstractIn 1912, Max von Laue and collaborators first observed diffraction spots from a millimeter-sized crystal of copper sulfate using an X-ray tube. Crystallography was born of this experiment, and since then, diffraction by both X-rays and electrons has revealed a myriad of inorganic and organic structures, including structures of complex protein assemblies. Advancements in X-ray sources have spurred a revolution in structure determination, facilitated by the development of new methods. This review explores some of the frontier methods that are shaping the future of X-ray diffraction, including coherent diffractive imaging, serial femtosecond X-ray crystallography and small-angle X-ray scattering. Collectively, these methods expand the current limits of structure determination in biological systems across multiple length and time scales.

scholarly journals Picosecond time-resolved X-ray diffraction from laser-shocked semiconductors

2004 ◽  
Vol 22 (3) ◽  
pp. 285-288 ◽  
Author(s):  
KAZUTAKA G. NAKAMURA ◽  
YOICHIRO HIRONAKA ◽  
HIDETAKA KAWANO ◽  
HIROAKI KISHIMURA ◽  
KEN-ICHI KONDO
Keyword(s):  
Shock Wave ◽  
Wave Propagation ◽  
Structural Dynamics ◽  
Lattice Deformation ◽  
X Rays ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Femtosecond Laser Beam ◽  
Diffraction Patterns

Ultrashort pulsed hard X rays are generated by focusing an intense femtosecond laser beam onto metal targets. Kαemissions are obtained from a Cu target. Picosecond time-resolved X-ray diffraction is performed to investigate structural dynamics of laser-shocked semiconductors using the laser plasma X-ray pulses. Lattice deformation associated with shock-wave propagation is directly observed. Evolution of strain profiles inside the crystal is determined without disturbance from the time-resolved X-ray diffraction patterns.

scholarly journals Report on a project on three-dimensional imaging of the biological cell by single-particle X-ray diffraction

2007 ◽  
Vol 64 (1) ◽  
pp. 33-35 ◽  
Author(s):  
D. Sayre
Keyword(s):  
Single Particle ◽  
High Vacuum ◽  
Three Dimensional ◽  
X Rays ◽  
X Ray Diffraction ◽  
Acta Cryst ◽  
Three Dimensional Imaging ◽  
X Ray ◽  
X Ray Crystallography ◽  
A Cell

Single-particle X-ray diffraction is an extension of X-ray crystallography which allows the specimen to be any small solid-state bounded object; in Shapiroet al.[Proc. Natl Acad. Sci. USA(2005),102, 15343–15346] and Thibaultet al.[Acta Cryst.(2006), A62, 248–261], the reader can find descriptions of a recent StonyBrook/Berkeley/Cornell two-dimensional imaging of a yeast cell by this technique. Our present work is aimed at extending the technique to the three-dimensional imaging of a cell. However, the usual method of doing that, namely rotating the specimen into many orientations in the X-ray beam, has not as yet given sufficiently good three-dimensional diffraction data to allow the work to go forward, the largest problem being the difficulty of preventing unwanted levels of change in the specimen through the extended exposure to a hostile environment of X-rays and, in some cases, high vacuum and/or extreme cold. The present paper discusses possible methods of dealing with this problem.

scholarly journals Molecular Structure and Its Inverse: The Mystery of Their Origins, the Enigma of Their Detection

2021 ◽  
pp. 45-51
Author(s):  
Sosale Chandrasekhar
Keyword(s):  
Absolute Configuration ◽  
Anomalous Dispersion ◽  
X Rays ◽  
X Ray Diffraction ◽  
Dispersion Method ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Absolute ◽  
Dispersion Technique ◽  
Stereogenic Center

The origins of the molecular-chiral homogeneity that is the very basis of life remain a tantalizing mystery. Molecular chirality itself is manifest in its interaction with radiation, particularly as optical activity, although an intriguing alternative technique based in X-ray crystallography is being increasingly employed. Thus, X-ray diffraction with anomalous dispersion is currently believed to lead to the absolute configuration of a stereogenic center, the ultimate goal of structural chemistry. However, despite its apparently unerring consistency, the fundamental basis of the anomalous dispersion technique is itself enigmatic. This is because it is unclear how the technique not only distinguishes two enantiomeric lattices but also assigns the absolute configuration: all, apparently, in the absence of an external chiral influence! Indeed, as argued previously, it is highly likely that the technique succeeds because the X-rays employed are circularly polarized, itself a possible consequence of parity violation. All the same, the question of how the absolute configuration is assigned remains, as the chiral sense of the putative circular polarization of the X-rays is unknown. It is argued herein that the anomalous dispersion method is essentially based in the chirality of X-rays that must have entered–although unbeknownst as such–into the calculations leading to the absolute configuration. In fact, the enigma surrounding the anomalous dispersion method derives from uncertainties concerning the theory of X-ray diffraction itself, thus leading to the apparently inescapable conclusion that both methods are essentially empirical — but without detracting from the brilliance of the scientific achievements that led to these methods.          

X-ray diffraction properties of curved crystal diffractors

1992 ◽  
Vol 50 (2) ◽  
pp. 1734-1735
Author(s):  
W. Z. Chang ◽  
D. B. Wittry
Keyword(s):  
Diffraction Theory ◽  
X Rays ◽  
Diffraction Image ◽  
X Ray Diffraction ◽  
Rocking Curve ◽  
X Ray ◽  
Bent Crystal ◽  
Diffraction Geometry ◽  
Crystal Parameter ◽  
Quantitative Procedure

Since Du Mond and Kirkpatrick first discussed the principle of a bent crystal spectrograph in 1930, curved single crystals have been widely utilized as spectrometric monochromators as well as diffractors for focusing x rays diverging from a point. Curved crystal diffraction theory predicts that the diffraction parameters - the rocking curve width w, and the peak reflection coefficient r of curved crystals will certainly deviate from those of their flat form. Due to a lack of curved crystal parameter data in current literature and the need for optimizing the choice of diffraction geometry and crystal materials for various applications, we have continued the investigation of our technique presented at the last conference. In the present abstract, we describe a more rigorous and quantitative procedure for measuring the parameters of curved crystals.The diffraction image of a singly bent crystal under study can be obtained by using the Johann geometry with an x-ray point source.

Investigation of the phase shift in X-ray forward diffraction using an X-ray interferometer

1998 ◽  
Vol 5 (3) ◽  
pp. 967-968 ◽  
Author(s):  
Keiichi Hirano ◽  
Atsushi Momose
Keyword(s):  
Phase Shift ◽  
Silicon Crystal ◽  
Dynamical Theory ◽  
Perfect Crystal ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Bragg Geometry

The phase shift of forward-diffracted X-rays by a perfect crystal is discussed on the basis of the dynamical theory of X-ray diffraction. By means of a triple Laue-case X-ray interferometer, the phase shift of forward-diffracted X-rays by a silicon crystal in the Bragg geometry was investigated.

scholarly journals X-ray crystal structure of a malonate-semialdehyde dehydrogenase fromPseudomonassp. strain AAC

2017 ◽  
Vol 73 (1) ◽  
pp. 24-28 ◽  
Author(s):  
Matthew Wilding ◽  
Colin Scott ◽  
Thomas S. Peat ◽  
Janet Newman
Keyword(s):  
Crystal Structure ◽  
Search Model ◽  
Molecular Replacement ◽  
X Rays ◽  
X Ray Diffraction ◽  
Acetyl Coa ◽  
Space Group ◽  
X Ray ◽  
Semialdehyde Dehydrogenase

The NAD-dependent malonate-semialdehyde dehydrogenase KES23460 fromPseudomonassp. strain AAC makes up half of a bicistronic operon responsible for β-alanine catabolism to produce acetyl-CoA. The KES23460 protein has been heterologously expressed, purified and used to generate crystals suitable for X-ray diffraction studies. The crystals belonged to space groupP212121and diffracted X-rays to beyond 3 Å resolution using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4zz7 as the search model.

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.

Synthesis and characterization of a linked, π-π stacked organotin compound of 2-mercapto-6-nitrobenzothiazolyl diphenyltin chloride with 2-ethoxyl-6-nitrobenzothiazole

2003 ◽  
Vol 81 (7) ◽  
pp. 825-831 ◽  
Author(s):  
Chunlin Ma ◽  
Qin Jiang ◽  
Rufen Zhang
Keyword(s):  
Title Compound ◽  
Organotin Compound ◽  
X Ray Diffraction ◽  
X Ray ◽  
Stacking Interaction ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Molecular Components

The new organotin compound, Ph2Sn(Cl)[S(C7H3N2O2S)]·[(C7H3N2O2S)OEt], assembled by an intermolecular aromatic benzothiazole–benzothiazole π-π stacking interaction, has been synthesized by the reaction of diphenyltin dichloride with 2-mercapto-6-nitrobenzothiazole. The title compound was characterized by elemental, IR, 1H NMR, and X-ray crystallography analyses. Single-crystal X-ray diffraction data reveals that the title compound has two different molecular components. The component Ph2Sn(Cl)[S(C7H3N2O2S)] has a pentacoordinate tin, which further forms an infinite one-dimensional chain by intermolecular non-bonded Cl···S interactions, resulting in an intercalation lattice that holds (C7H3N2O2S)OEt molecules. The formation of the molecule (C7H3N2O2S)OEt as well as its intercalated mechanism has also been discussed.Key words: organotin, assemble, π-π stacking interaction, 2-mercapto-6-nitrobenzothiazole, non-bonded interaction, crystal structure.

Sign in / Sign up

Export Citation Format

Share Document