Large-angle convergent-beam setup for femtosecond X-ray crystallography

2003 ◽  
Vol 36 (2) ◽  
pp. 348-349 ◽  
Author(s):  
Davide Boschetto ◽  
Christian Rischel ◽  
I. Uschmann ◽  
J. Perez ◽  
S. Fourmaux ◽  
...  
Keyword(s):  
Small Molecule ◽  
Large Angle ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Beam Geometry ◽  
Convergent Beam ◽  
The Way

It is demonstrated how femtosecond plasma X-ray sources can be used to record X-ray diffraction images with many simultaneous reflections. A convergent-beam geometry was implemented and tested with a crystal of a small molecule [Fe-py3(tren)] as well as with a crystal of the protein lysozyme. The results pave the way for femtosecond X-ray crystallography.

Reminiscences and discoveries: Dorothy Hodgkin and the Indian connection

1996 ◽  
Vol 50 (1) ◽  
pp. 115-127 ◽  
Keyword(s):  
Large Angle ◽  
Direct Methods ◽  
Statistical Fluctuation ◽  
Organic Crystals ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Angle Scattering ◽  
Molecular Sizes ◽  
Indian Institute Of Science

Dorothy Hodgkin - as crystallographer, scientist and human being - far surpasses most, and so it is not easy to write about her many-splendoured personality. Instead, my aim here will he to discuss her influence on the growth of X-ray crystallography in India, directly through those who worked with her and indirectly by her travelling all over this country. In such an account, one must be pardoned for some personal element creeping in. In the twenties, India had developed a fairly strong tradition in X-ray physics. The six-week visit of C.V. Raman to Europe in 1921 greatly changed his research interests. On seeing the blue of the Mediterranean he started his researches on the scattering of light in liquids which finally culminated in the discovery of what is now called the Raman Effect. His encounter with Sir William Bragg and his work on naphthalene structure started three lines of research in India. First, Raman fabricated an X-ray tube and was amongst the earliest to use X-ray diffraction as a structural tool to study liquids. He showed that while in large-angle scattering the haloes reflected specific molecular sizes and packing shapes, small-angle scattering was directly related to the statistical fluctuation of density in a liquid. Second, Raman knew that Bragg’s first structure of naphthalene was not consistent with its birefringence, while the second one was. With this as cue he and his school launched extensive studies on the optical and magnetic anisotropy of organic crystals to get vital information on the arrangements of molecules in the crystalline state. Third, one of his students, Kedareshwar Bannerjee, was amongst the earliest to probe into the problem of phase determination by direct methods and for this he used Bragg’s data on naphthalene. Unfortunately, in spite of this early lead, it was not until 1951 that the first crystal structure was solved in India using Fourier methods by Gopinath Kartha. The Indian Institute of Science (IISc) had great hopes of starting a powerful school of X-ray crystallography when G.N. Ramachandran came back from Cambridge. But he went over to Madras, and there he established one of the most renowned Schools of Biophysics. With Gopinath Kartha he solved the structure of collagen.

Application of convergent-beam illumination methods to the study of lattice distortion across the interface

1992 ◽  
Vol 50 (1) ◽  
pp. 232-233
Author(s):  
Zuzanna Liliental-Weber ◽  
T. Kaneyama ◽  
M. Terauchi ◽  
M. Tanaka
Keyword(s):  
Spatial Resolution ◽  
Lattice Distortion ◽  
Large Angle ◽  
Lattice Parameter ◽  
Gaas Layer ◽  
X Ray Diffraction ◽  
X Ray ◽  
Accuracy Measurement ◽  
The Difference ◽  
Convergent Beam

A high accuracy measurement of the lattice parameter can be obtained by x-ray diffraction. However, these methods have low spatial resolution and are limited by sample thickness. Therefore, for heterolayers much better information about local distortions near the interface can be obtained by electron microscopy using convergent-beam illumination. Large-angle convergent-beam electron diffraction (LACBED) patterns and convergent-beam imaging (CBIM) were applied to study of the lattice distortion across the interface of the GaAs epilayer grown on [001] GaAs substrate and the GaAs layer grown at 200°C (called the low-temperature (LT) layer). These LT GaAs layers are grown by molecular beam epitaxy from As oversaturation and are known to be As rich. Particle-induced x-ray studies reveal up to 1.5 % extra As. This excess As leads to the expansion of the lattice parameter up to 0.15% when measured by x-ray diffraction along the (004) reflection. From this study, it was expected that a cubic expansion of the lattice parameter would be equal in all three directions. However, TEM studies do not reveal the formation of dislocations at the interface, which would be expected taking into account the difference in the lattice parameter across the interface . Convergence beam illumination methods were applied to study in detail the strain, lattice parameter variation, and crystallographic distortion across the interface, since these methods have spatial resolution several orders of magnitude higher than x-ray diffraction. A CBED pattern taken in the substrate and in the layer with an incidence close to the [530] direction (exact orientation [0.869 0.495 0]) reveals the lattice parameter change, since the position of the cross of the 1113 and 1113 lines changes when an electron beam is placed in the substrate and the layer, respectively (Fig. la,b).

X-ray multislice computation using the Moodie–Wagenfeld equations: divergent-beam pattern simulation in three-beam and six-beam Laue cases

1999 ◽  
Vol 55 (2) ◽  
pp. 246-257
Author(s):  
P. Goodman ◽  
Linda Liu
Keyword(s):  
Electron Diffraction ◽  
Rapid Development ◽  
Heavy Atom ◽  
Large Angle ◽  
X Ray Diffraction ◽  
Divergent Beam ◽  
X Ray ◽  
Voltage Electron ◽  
Chiral Interaction ◽  
Convergent Beam

Pattern simulations for three-beam and six-beam X-ray diffraction are presented using multislice calculations based on Moodie & Wagenfeld's formulation of the X-ray equations, which factorize Maxwell's equations into Dirac format, using circular-polarization bases. The results are presented in three forms: one-dimensional rocking curves, Pendellösung thickness fringes, and convergent/divergent-beam patterns of single-diffraction orders, using experience gained from CBED (convergent-beam electron diffraction) and LACBED (large-angle CBED) techniques developed for high-voltage electron diffraction transmission patterns. This latter and quite new technique displays the results in the most compact form. The acronym DBXRAD (divergent-beam X-ray diffraction) is used for these patterns. The optics required for these patterns has only recently become available for radiations up to Mo Kα1 in energy and for limited angular divergences, but with capillary focusing currently undergoing rapid development these limits are likely to be extended. However, these simulations define critical angular ranges within reach of current designs. Simulations for light- and heavy-atom structures belonging to the enantiomorphic space-group pair P3121 and P3221 provide clear evidence of chiral interaction between radiation and structure, highlighting divergences from the use in structure analysis of the well studied CBED pattern symmetries. Mo Kα1 and Ta Kα1 wavelengths were used to minimize absorption for the two structures studied, an important factor owing to the large thicknesses (up to 20 mm) required.

Microstructure and crystal symmetry of Pb2Sr2(Y/Ca)Cu3O9−δ

1990 ◽  
Vol 48 (4) ◽  
pp. 64-65
Author(s):  
Y. P. Lin ◽  
J. S. Xue ◽  
J. E. Greedan
Keyword(s):  
Electron Diffraction ◽  
High Temperature Superconductors ◽  
Carbon Film ◽  
Basic Structure ◽  
Crystal Symmetry ◽  
X Ray Diffraction ◽  
X Ray ◽  
Space Groups ◽  
New Family ◽  
Convergent Beam

A new family of high temperature superconductors based on Pb2Sr2YCu3O9−δ has recently been reported. One method of improving Tc has been to replace Y partially with Ca. Although the basic structure of this type of superconductors is known, the detailed structure is still unclear, and various space groups has been proposed. In our work, crystals of Pb2Sr2YCu3O9−δ with dimensions up to 1 × 1 × 0.25.mm and with Tc of 84 K have been grown and their superconducting properties described. The defects and crystal symmetry have been investigated using electron microscopy performed on crushed crystals supported on a holey carbon film.Electron diffraction confirmed x-ray diffraction results which showed that the crystals are primitive orthorhombic with a=0.5383, b=0.5423 and c=1.5765 nm. Convergent Beam Electron Diffraction (CBED) patterns for the and axes are shown in Figs. 1 and 2 respectively.

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.

scholarly journals Compressibility Studies of Zirconium Based Metal-Organic Frameworks

2014 ◽  
Vol 70 (a1) ◽  
pp. C157-C157
Author(s):  
Claire Hobday ◽  
Stephen Moggach ◽  
Carole Morrison ◽  
Tina Duren ◽  
Ross Forgan
Keyword(s):  
High Pressure ◽  
Mechanical Stability ◽  
Metal Organic Frameworks ◽  
External Pressure ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Pressure Medium ◽  
Metal Organic ◽  
University Of Oslo

Metal-organic frameworks (MOFs) are a well-studied class of porous materials with the potential to be used in many applications such as gas storage and catalysis.[1] UiO-67 (UiO = University of Oslo), a MOF built from zirconium oxide units connected with 4,4-biphenyldicarboxylate (BDC) linkers, forms a face centred cubic structure. Zirconium has a high affinity towards oxygen ligands making these bridges very strong, resulting in UiO-based MOFs having high chemical and thermal stability compared to other MOF structures. Moreover, UiO-67 has become popular in engineering studies due to its high mechanical stability.[2] Using high pressure x-ray crystallography we can exert MOFs to GPa pressures, experimentally exploring the mechanical stability of MOFs to external pressure. By immersing the crystal in a hydrostatic medium, pressure is applied evenly to the crystal. On surrounding a porous MOF with a hydrostatic medium composed of small molecules (e.g. methanol), the medium can penetrate the MOF, resulting in medium-dependant compression. On compressing MOF-5 (Zn4O(BDC)3) using diethylformamide as a penetrating medium, the framework was shown to have an increased resistance to compression, becoming amorphous several orders of magnitude higher in pressure than observed on grinding the sample.[3] Here we present a high-pressure x-ray diffraction study on the UiO-based MOF UiO-67, and several new synthesised derivatives built from same metal node but with altered organic linkers, allowing us to study in a systematic way, the mechanical stability of the MOF, and its pressure dependence on both the linker, and pressure medium.

scholarly journals Human insulin polymorphism upon ligand binding and pH variation: the case of 4-ethylresorcinol

IUCrJ ◽  
2015 ◽  
Vol 2 (5) ◽  
pp. 534-544 ◽  
Author(s):  
S. Fili ◽  
A. Valmas ◽  
M. Norrman ◽  
G. Schluckebier ◽  
D. Beckers ◽  
...  
Keyword(s):  
Human Insulin ◽  
Organic Ligand ◽  
European Synchrotron Radiation Facility ◽  
X Ray Diffraction ◽  
Ph Variation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Swiss Light Source ◽  
Crystallization Experiments ◽  
Ph Range

This study focuses on the effects of the organic ligand 4-ethylresorcinol on the crystal structure of human insulin using powder X-ray crystallography. For this purpose, systematic crystallization experiments have been conducted in the presence of the organic ligand and zinc ions within the pH range 4.50–8.20, while observing crystallization behaviour around the isoelectric point of insulin. High-throughput crystal screening was performed using a laboratory X-ray diffraction system. The most representative samples were selected for synchrotron X-ray diffraction measurements, which took place at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS). Four different crystalline polymorphs have been identified. Among these, two new phases with monoclinic symmetry have been found, which are targets for the future development of microcrystalline insulin drugs.

scholarly journals The Use of Connected Masks for Reconstructing the Single Particle Image from X-Ray Diffraction Data. II. The Dependence of the Accuracy of the Solution on the Sampling Step of Experimental Data

2015 ◽  
Vol 10 (2) ◽  
pp. 508-525 ◽  
Author(s):  
Н.Л. Лунина ◽  
N.L. Lunina
Keyword(s):  
Experimental Data ◽  
Particle Image ◽  
Expected Improvement ◽  
Problem Solution ◽  
Phase Problem ◽  
X Ray Diffraction ◽  
Sampling Step ◽  
X Ray ◽  
X Ray Crystallography ◽  
Grid Points

Advances in the methodology of the X-ray diffraction experiments leads to a possibility to register the rays scattered by large isolated biological particles (viruses and individual cells) but not only by crystalline samples. The experiment with an isolated particle provides researchers with the intensities of the scattered rays for the continuous spectrum of scattering vectors. Such experiment gives much more experimental data than an experiment with a crystalline sample where the information is limited to a set of Bragg reflections. This opens up additional opportunities in solving underlying problem of X-ray crystallography, namely, calculating phase values for the scattered waves needed to restore the structure of the object under study. In practice, the original continuous diffraction pattern is sampled, reduced to the values at grid points in the space of scattering vectors (in the reciprocal space). The sampling step determines the amount of the information involved in solving the phase problem and the complexity of the necessary calculations. In this paper, we investigate the effect of the sampling step on the accuracy of the phase problem solution obtained by the method proposed earlier by the authors. It is shown that an expected improvement of the accuracy of the solution with the reducing the sampling step continues even after crossing the Nyquist limit defined as the inverse of the double size of the object under study.

scholarly journals Low-Zpolymer sample supports for fixed-target serial femtosecond X-ray crystallography

2015 ◽  
Vol 48 (4) ◽  
pp. 1072-1079 ◽  
Author(s):  
Geoffrey K. Feld ◽  
Michael Heymann ◽  
W. Henry Benner ◽  
Tommaso Pardini ◽  
Ching-Ju Tsai ◽  
...  
Keyword(s):  
Protective Antigen ◽  
Three Dimensional ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Fixed Target ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transmission Electron ◽  
Linac Coherent Light Source ◽  
Efficient Alternative

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introductionviaa translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Zplastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. The benefits and limitations of these low-Zfixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.

scholarly journals NMR and X-ray studies of apetalic acid isolated from Calophyllum brasiliense and of its chiral amides

2021 ◽  
Author(s):  
Marie-Rose Van Calsteren ◽  
Ricardo Reyes-Chilpa ◽  
Chistopher K Jankowski ◽  
Fleur Gagnon ◽  
Simón Hernández-Ortega ◽  
...  
Keyword(s):  
Antimycobacterial Activity ◽  
Side Chain ◽  
Carboxyl Group ◽  
X Ray Diffraction ◽  
Rain Forests ◽  
X Ray ◽  
X Ray Crystallography ◽  
Calophyllum Brasiliense ◽  
Derivatives Of

The tropical tree Calophyllum brasiliense (Clusiaceae) grows in the rain forests from Brazil to Mexico. Its leaves, as well as those of other Calophyllum species, are rich sources of chromanone acids, such as apetalic acid, isoapetalic acid, and their derivatives. Apetalic acid has shown significant antimycobacterial activity. The biological activity of apetalic acid has been related to the configuration of three asymmetric centers and the stereochemistry of the molecule; however, the C-19 configuration in the acidic side chain has not been fully resolved. For this reason, the unequivocal determination of the absolute configuration by means of X-ray crystallography in a sample of unique homogeneous apetalic acid stereoisomer was the most important point to start this study. We prepared some chiral amides using the carboxyl group. We determined the C-19 stereochemistry of apetalic acid, and its specific chiral derivatives, using NMR, X-ray diffraction methods, and molecular mechanics. Finally, we observed that steric hindrance in the side chain of apetalic acid leads to restriction of rotation around the pivotal link C-10 and C-19 establishing chiral centers at C2(R), C3(S), and C19(R). We were able to separate derivatives of these two high-rotatory-barrier conformers of apetalic acid by forming diastereoisomeric amides with phenylglycine methyl ester having a chiral center at C-2’. Our results allowed the conclusion of the existence of atropisomerism in the apetalic acid molecule.

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