The hydrolytic water molecule in trypsin, revealed by time-resolved Laue crystallography

Science ◽  
1993 ◽  
Vol 259 (5095) ◽  
pp. 669-673 ◽  
Author(s):  
PT Singer ◽  
A Smalas ◽  
RP Carty ◽  
WF Mangel ◽  
RM Sweet
Keyword(s):  
Water Molecule ◽  
Three Dimensional ◽  
Initial Step ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Density Maps ◽  
Before And After ◽  
Ph Jump ◽  
Hydrolysis Of

Crystals of bovine trypsin were acylated at the reactive residue, serine 195, to form the transiently stable p-guanidinobenzoate. Hydrolysis of this species was triggered in the crystals by a jump in pH. The hydrolysis was monitored by three-dimensional Laue crystallography, resulting in three x-ray diffraction structures, all from the same crystal and each representing approximately 5 seconds of x-ray exposure. The structures were analyzed at a nominal resolution of 1.8 angstroms and were of sufficient quality to reproduce subtle features in the electron-density maps for each of the structures. Comparison of the structures before and after the pH jump reveals that a water molecule has positioned itself to attack the acyl group in the initial step of the hydrolysis of this transient intermediate.

scholarly journals In Situ Coherent X-ray Diffraction during Three-Point Bending of a Au Nanowire: Visualization and Quantification

2018 ◽  
Vol 2 (4) ◽  
pp. 24 ◽  
Author(s):  
Anton Davydok ◽  
Thomas Cornelius ◽  
Zhe Ren ◽  
Cedric Leclere ◽  
Gilbert Chahine ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Reciprocal Space ◽  
X Ray Diffraction ◽  
Complex Deformation ◽  
X Ray ◽  
Three Point Bending ◽  
Atomic Force ◽  
Au Nanowire ◽  
Before And After

The three-point bending behavior of a single Au nanowire deformed by an atomic force microscope was monitored by coherent X-ray diffraction using a sub-micrometer sized hard X-ray beam. Three-dimensional reciprocal-space maps were recorded before and after deformation by standard rocking curves and were measured by scanning the energy of the incident X-ray beam during deformation at different loading stages. The mechanical behavior of the nanowire was visualized in reciprocal space and a complex deformation mechanism is described. In addition to the expected bending of the nanowire, torsion was detected. Bending and torsion angles were quantified from the high-resolution diffraction data.

A one-dimensional coordination polymer based on Cd2O2clusters: poly[aqua(μ3-4,4′-sulfonyldibenzoato)(3,4,7,8-tetramethyl-1,10-phenanthroline-κ2N,N′)cadmium(II)]

2013 ◽  
Vol 69 (3) ◽  
pp. 244-246 ◽  
Author(s):  
Jian-Qing Tao
Keyword(s):  
Water Molecule ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Chain Polymer ◽  
One Dimensional ◽  
X Ray ◽  
Acid Ligand ◽  
Carboxylate Groups ◽  
Metal Organic ◽  
Coordinated Water

In the title mixed-ligand metal–organic polymeric complex [Cd(C14H8O6S)(C16H16N2)(H2O)]n, the asymmetric unit contains a crystallographically unique CdIIatom, one doubly deprotonated 4,4′-sulfonyldibenzoic acid ligand (H2SDBA), one 3,4,7,8-tetramethyl-1,10-phenanthroline (TMPHEN) molecule and one water molecule. Each CdIIcentre is coordinated by two N atoms from the chelating TMPHEN ligand, three O atoms from monodentate carboxylate groups of three different SDBA2−ligands and one O atom from a coordinated water molecule, giving a distorted CdN2O4octahedral geometry. Single-crystal X-ray diffraction analysis reveals that the compound is a one-dimensional double-chain polymer containing 28-membered rings based on Cd2O2clusters, with a Cd...Cd separation of 3.6889 (4) Å. These chains are linked by O—H...O and C—H...O hydrogen bonds to form a three-dimensional supramolecular framework. The framework is reinforced by π–π and C—O...π interactions.

Static Laue Diffraction Studies on Acetylcholinesterase

1998 ◽  
Vol 54 (6) ◽  
pp. 1359-1366 ◽  
Author(s):  
Raimond B. G. Ravelli ◽  
Mia L. Raves ◽  
Zhong Ren ◽  
Dominique Bourgeois ◽  
Michel Roth ◽  
...  
Keyword(s):  
Structural Change ◽  
Exposure Time ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Reversible Inhibitor ◽  
Data Set ◽  
Time Resolved ◽  
X Ray ◽  
Density Maps

Acetylcholinesterase (AChE) is one of nature's fastest enzymes, despite the fact that its three-dimensional structure reveals its active site to be deeply sequestered within the molecule. This raises questions with respect to traffic of substrate to, and products from, the active site, which may be investigated by time-resolved crystallography. In order to address one aspect of the feasibility of performing time-resolved studies on AChE, a data set has been collected using the Laue technique on a trigonal crystal of Torpedo californica AChE soaked with the reversible inhibitor edrophonium, using a total X-ray exposure time of 24 ms. Electron-density maps obtained from the Laue data, which are of surprisingly good quality compared with similar maps from monochromatic data, show essentially the same features. They clearly reveal the bound ligand, as well as a structural change in the conformation of the active-site Ser200 induced upon binding.

scholarly journals Unveiling the spatial distribution of molecular coherences at conical intersections by covariance X-ray diffraction signals

2021 ◽  
Vol 118 (22) ◽  
pp. e2105046118
Author(s):  
Stefano M. Cavaletto ◽  
Daniel Keefer ◽  
Jérémy R. Rouxel ◽  
Flavia Aleotti ◽  
Francesco Segatta ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Three Dimensional ◽  
Laser Pulses ◽  
Conical Intersection ◽  
Conical Intersections ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Diffraction Imaging ◽  
The Rich

The outcomes and timescales of molecular nonadiabatic dynamics are decisively impacted by the quantum coherences generated at localized molecular regions. In time-resolved X-ray diffraction imaging, these coherences create distinct signatures via inelastic photon scattering, but they are buried under much stronger background elastic features. Here, we exploit the rich dynamical information encoded in the inelastic patterns, which we reveal by frequency-dispersed covariance ultrafast powder X-ray diffraction of stochastic X-ray free-electron laser pulses. This is demonstrated for the photoisomerization of azobenzene involving the passage through a conical intersection, where the nuclear wave packet branches and explores different quantum pathways. Snapshots of the coherence dynamics are obtained at high frequency shifts, not accessible with conventional diffraction measurements. These provide access to the timing and to the confined spatial distribution of the valence electrons directly involved in the conical intersection passage. This study can be extended to full three-dimensional imaging of conical intersections with ultrafast X-ray and electron diffraction.

Study of The Hydrothermal Synthesis of Gallium Phosphates Using in Situ Time-Resolved X-Ray Diffraction

1998 ◽  
Vol 547 ◽  
Author(s):  
R.I. Walton ◽  
T. Loiseau ◽  
R.J. Francis ◽  
D. O'Hare ◽  
G. Férey
Keyword(s):  
Kinetic Data ◽  
Three Dimensional ◽  
Diffraction Method ◽  
Effect Of Temperature ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
Time Resolved ◽  
X Ray ◽  
Phosphorus Source

AbstractThe hydrothermal crystallisation (130-180 °C) of three-dimensional open-framework gallium and aluminium oxyfluoro-phosphates with the ULM-3 and ULM-4 structures have been studied in situ for the first time. The in situ energy-dispersive X-ray diffraction method has allowed the formation of the crystalline products to be observed under hydrothermal conditions The integrated areas of the strongest Bragg reflections has allowed quantitative kinetic data to be extracted. The effect of temperature, phosphorus source, templating agent have been investigated. The nature of phosphorus source in the reaction mixture has been found to affect dramatically the course of reaction for certain combinations of amine and temperature. Previously unobserved transient crystalline phases have been seen during the production of ULM-3 gallium phosphates when P2O5 or polyphosphoric acid are used. The formation of these intermediates affects the kinetics of product growth. In the case of the aluminium ULM-3 materials reaction always proceeds via a crystalline intermediate whatever phosphorus source is used. The ULM-4 framework materials are found to always crystallise directly with no evidence for any intermediates. Kinetic data for each system have been modelled using standard solid-state chemistry expressions, and these calculations indicate the reactions to be diffusion controlled.

The crystal structure of a pyridine-vermiculite complex

Clay Minerals ◽  
1967 ◽  
Vol 7 (2) ◽  
pp. 145-153 ◽  
Author(s):  
K. Susa ◽  
H. Steinfink ◽  
W. F. Bradley
Keyword(s):  
Cation Exchange Capacity ◽  
Three Dimensional ◽  
Exchange Capacity ◽  
Water Molecules ◽  
Hydrogen Ions ◽  
X Ray Diffraction ◽  
Difference Electron Density ◽  
Cell Water ◽  
X Ray ◽  
Density Maps

AbstractA pyridine-vermiculite complex has been investigated by three dimensional X-ray diffraction techniques. The preparation of the complex was carried out at a pH ∼ 4 using a solution of pyridinium hydrochloride. Exsolved magnesium from the octahedral positions satisfied approximately one-half of the cation exchange capacity. The rest of the exchange capacity is satisfied by hydrogen ions and pyridinium ions which are statistically distributed over crystallographic sites so that less than three electrons per Å3 are present at any given point. Three dimensional difference electron density maps did not locate the carbon atoms except to indicate that the organic molecule occupies positions in the true and in the two pseudo mirror planes in the unit cell. Water molecules were present in the interlayer in octahedral arrangement around the cation as in the natural mineral.

scholarly journals Beyond a phenomenological description of magnetostriction

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
A. H. Reid ◽  
X. Shen ◽  
P. Maldonado ◽  
T. Chase ◽  
E. Jal ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Magnetic Order ◽  
Three Dimensional ◽  
Fept Nanoparticles ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Fs Laser ◽  
The Time Domain ◽  
Microscopic Origin

Abstract Magnetostriction, the strain induced by a change in magnetization, is a universal effect in magnetic materials. Owing to the difficulty in unraveling its microscopic origin, it has been largely treated phenomenologically. Here, we show how the source of magnetostriction—the underlying magnetoelastic stress—can be separated in the time domain, opening the door for an atomistic understanding. X-ray and electron diffraction are used to separate the sub-picosecond spin and lattice responses of FePt nanoparticles. Following excitation with a 50-fs laser pulse, time-resolved X-ray diffraction demonstrates that magnetic order is lost within the nanoparticles with a time constant of 146 fs. Ultrafast electron diffraction reveals that this demagnetization is followed by an anisotropic, three-dimensional lattice motion. Analysis of the size, speed, and symmetry of the lattice motion, together with ab initio calculations accounting for the stresses due to electrons and phonons, allow us to reveal the magnetoelastic stress generated by demagnetization.

Raman Spectrum of Ultrafine Anatase Powders Derived from Hydrolysis of Alkoxide

1998 ◽  
Vol 52 (5) ◽  
pp. 673-678 ◽  
Author(s):  
Yasuo Iida ◽  
Masamichi Furukawa ◽  
Tsutomu Aoki ◽  
Tadao Sakai
Keyword(s):  
Defect Density ◽  
Three Dimensional ◽  
Finite Size ◽  
Close Relation ◽  
Titanium Isopropoxide ◽  
Scaling Exponent ◽  
Organic Residue ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrolysis Of

Ultrafine, nanometer-sized anatase particles were prepared by the hydrolysis of titanium isopropoxide. Their Raman spectra are discussed in view of the finite size effects. The crystallite size D estimated by the X-ray diffraction peaks (Scherrer method) was found to be correlated with the Raman peak width Γ. The relationship could be expressed in the empirical equation, Γ = Γ0 + kD−α with the scaling exponent α of 1.5. Because the anatase crystal spans a three-dimensional network, the result demonstrates that 2× α is equal to the dimensionality of the sample. In addition, the anatase powders prepared by different hydrolysis schemes regressed into curves with different constant terms γ0 and k. The amount of organic residue was mainly affected by the hydrolysis scheme, and the organic residue caused the formation of defects in the crystalline particle by the following heat treatment. Therefore, it is obvious that the variation in Γ0 and k has a close relation to the defect density of the crystalline particles. The defect densities were estimated by using the correlation between the X-ray diffraction and the Raman data.

Nanoscale stability of two- and three-dimensional defects in Cu/Ag–Mo thin films

2017 ◽  
Vol 50 (1) ◽  
pp. 152-171 ◽  
Author(s):  
G. Csiszár ◽  
A. Makvandi ◽  
E. J. Mittemeijer
Keyword(s):  
Thin Films ◽  
Heat Treatment ◽  
Texture Evolution ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Twin Boundaries ◽  
X Ray ◽  
Transmission Electron ◽  
Before And After ◽  
Columnar Grain

A comparative study of the thermal stability of nanocrystalline Cu–Mo and Ag–Mo alloy thin films was performed. Phase decomposition, texture evolution, grain coarsening and segregation of Mo to planar faults of both films, before and after heat treatment, were studied using X-ray diffraction measurements and (high-resolution) transmission electron microscopy with energy-dispersive spectroscopy. The evolution of stress/strain in the thin films was traced by in situ X-ray diffraction measurements. The segregation of Mo solute atoms at twin boundaries in both films already occurs at room temperature. By first segregation and then precipitation of Mo atoms at grain boundaries, the columnar grain microstructure is preserved upon heat treatment. In the case of Ag–Mo thin films, the twin boundaries are also more or less preserved at elevated temperature, but in the case of Cu–Mo thin films the annihilation of twin boundaries takes place concomitantly with the precipitation of Mo in columnar grain interiors.

scholarly journals In-Situ Coherent X-Ray Diffraction during Three-Point Bending of a Au Nanowire: Visualization and Quantification

2018 ◽  
Author(s):  
Anton Davydok ◽  
Thomas W. Cornelius ◽  
Zhe Ren ◽  
Cedric Leclere ◽  
Gilbert Chahine ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Reciprocal Space ◽  
X Ray Diffraction ◽  
Complex Deformation ◽  
X Ray ◽  
Three Point Bending ◽  
Atomic Force ◽  
Au Nanowire ◽  
Before And After

The three-point bending behavior of a single Au nanowire deformed with an atomic force microscope was monitored by coherent X-ray diffraction using a sub-micrometer sized hard X-ray beam. While three-dimensional reciprocal-space maps were recorded before and after deformation by standard rocking curves, they were measured by scanning the energy of the incident X-ray beam during deformation at different loading stages. The mechanical behavior of the nanowire is visualized in reciprocal space and a complex deformation mechanism is described. In addition to the expected bending of the nanowire, torsion is detected. Bending and torsion angles are quantified from the high resolution diffraction data.

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