viewSq, a Visual Molecular Dynamics (VMD) module for calculating, analyzing, and visualizing X-ray and neutron structure factors from atomistic simulations

Feasibility of isomorphous substitution in electron diffraction is supported by a calculation of the mean alteration of the electron-diffraction structure factors for hemoglobin crystals caused by substituting two mercury atoms per molecule, following Green, Ingram & Perutz, but with allowance for the proportionality of f to Z3/4 for electron diffraction. This yields a mean net change in F of 12.5%, as contrasted with 22.8% for x-ray diffraction.Use of the hydration chamber in electron diffraction opens prospects for examining many proteins that yield only very thin crystals not suitable for x-ray diffraction. Examination in the wet state avoids treatments that could cause translocation of the heavy-atom labels or distortion of the crystal. Combined with low-fluence techniques, it enables study of the protein in a state as close to native as possible.We have undertaken a study of crystals of rat hemoglobin by electron diffraction in the wet state. Rat hemoglobin offers a certain advantage for hydration-chamber work over other hemoglobins in that it can be crystallized from distilled water instead of salt solutions.

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Highlights in the history of X-ray topography1

Zeitschrift für Kristallographie - Crystalline Materials ◽

10.1524/zkri.1995.210.6.394 ◽

1995 ◽

Vol 210 (6) ◽

Author(s):

A. R. Lang

Keyword(s):

Magnetic Domain ◽

Diffraction Theory ◽

Dislocation Loops ◽

X Ray Diffraction ◽

X Ray ◽

Domain Structures ◽

Structure Factors ◽

History Of ◽

Dislocation Sources ◽

Non Destructive

AbstractX-ray topography provides a non-destructive method of mapping point-by-point variations in orientation and reflecting power within crystals. The discovery, made by several workers independently, that in nearly perfect crystals it was possible to detect individual dislocations by X-ray diffraction contrast started an epoch of rapid exploitation of X-ray topography as a new, general method for assessing crystal perfection. Another discovery, that of X-ray Pendellösung, led to important theoretical developments in X-ray diffraction theory and to a new and precise method for measuring structure factors on an absolute scale. Other highlights picked out for mention are studies of Frank-Read dislocation sources, the discovery of long dislocation helices and lines of coaxial dislocation loops in aluminium, of internal magnetic domain structures in Fe-3 wt.% Si, and of stacking faults in silicon and natural diamonds.

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Real-Space X-Ray Pair Distribution Function Analysis and Molecular-Dynamics Modelling of Diflunisal Channel Hydrates

10.26434/chemrxiv.12837524 ◽

2020 ◽

Author(s):

Anuradha Pallipurath ◽

Francesco Civati ◽

Jonathan Skelton ◽

Dean Keeble ◽

Clare Crowley ◽

...

Keyword(s):

Molecular Dynamics ◽

Distribution Function ◽

Structural Dynamics ◽

First Principles ◽

Pair Distribution Function ◽

Function Analysis ◽

Real Space ◽

X Ray ◽

Dynamics Modelling ◽

Dynamics Simulations

X-ray pair distribution function analysis is used with first-principles molecular dynamics simulations to study the co-operative H<sub>2</sub>O binding, structural dynamics and host-guest interactions in the channel hydrate of diflunisal.

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Faculty Opinions recommendation of Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1048003.498039 ◽

2006 ◽

Author(s):

D Peter Tieleman

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

K Channel ◽

Replica Exchange Molecular Dynamics ◽

X Ray ◽

X Ray Crystallography ◽

Dynamics Simulations

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Ultrafast Soft X-Ray Laser Probing of Core Level Molecular Dynamics

10.21236/ada419569 ◽

2003 ◽

Author(s):

Stephen R. Leone ◽

Veronica M. Bierbaum

Keyword(s):

Molecular Dynamics ◽

Core Level ◽

X Ray ◽

Laser Probing

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A synchrotron X-ray study of the electron density in C-type rare earth oxides

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768195013371 ◽

1996 ◽

Vol 52 (3) ◽

pp. 414-422 ◽

Cited By ~ 46

Author(s):

E. N. Maslen ◽

V. A. Streltsov ◽

N. Ishizawa

Keyword(s):

Heavy Metal ◽

Rare Earth ◽

Electron Density ◽

Approximate Symmetry ◽

Data Set ◽

X Ray ◽

Metal Atoms ◽

Structure Factors ◽

Deformation Electron Density ◽

Synthetic Crystals

Structure factors for small synthetic crystals of the C-type rare earth (RE) sesquioxides Y2O3, Dy2O3 and Ho2O3 were measured with focused λ = 0.7000 (2) Å, synchrotron X-radiation, and for Ho2O3 were re-measured with an MoKα (λ = 0.71073 Å) source. Approximate symmetry in the deformation electron density (Δρ) around a RE atom with pseudo-octahedral O coordination matches the cation geometry. Interactions between heavy metal atoms have a pronounced effect on the Δρ map. The electron-density symmetry around a second RE atom is also perturbed significantly by cation–anion interactions. The compounds magnetic properties reflect this complexity. Space group Ia{\bar 3}, cubic, Z = 16, T = 293 K: Y2O3, Mr = 225.82, a = 10.5981 (7) Å, V = 1190.4 (2) Å3, Dx = 5.040 Mg m−3, μ 0.7 = 37.01 mm−1, F(000) = 1632, R = 0.067, wR = 0.067, S = 9.0 (2) for 1098 unique reflections; Dy2O3, Mr = 373.00, a = 10.6706 (7) Å, V = 1215.0 (2) Å3, Dx = 8.156 Mg m−3, μ 0.7 = 44.84 mm−1, F(000) = 2496, R = 0.056, wR = 0.051, S = 7.5 (2) for 1113 unique reflections; Ho2O3, Mr = 377.86, a = 10.606 (2) Å, V = 1193.0 (7) Å3, Dx = 8.415 Mg m−3, μ 0.7 = 48.51 mm−1 F(000) = 2528, R = 0.072, wR = 0.045, S = 9.2 (2) for 1098 unique reflections of the synchrotron data set.

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