X-ray diffraction , laboratory

Lead screens for the protection of personnel in x-ray diffraction laboratories are usually at least 1 mm thick. Calculate the transmission factor (Arans./Ancidem) of such a screen for Cu Ka, Mo Ka, and the shortest wavelength radiation from a tube operated at 30,000 volts. 

Fig. 9.1. Modern area detector diffractometer (Bruker-Nonius Kappa APEX II) with sealed-tube Mo-radiation source and low-temperature cooling device in Jyvaskyla University X-ray diffraction laboratory. The blow-up picture shows the goniometer head into which the crystal under study has been mounted.

In the context of this review it is necessary to evaluate specifically those problems of membrane structure research which carry an essential requirement for the characteristics of synchrotron radiation. In other words, what problems are there which cannot, or only with great difficulty, be solved with the much cheaper facilities of an ordinary X-ray diffraction laboratory ... 

A diffractometer which performs only point measurements, does not give the cell constants unambiguously, since it deals only with discrete points in the reciprocal space. Continuous mens-urement in the reciprocal space is necessary to make certain that no essential points for unit cell determination have been missed. This fact, together with pedagogical considerations, is the reason that film techniques are still used in the X-ray diffraction laboratory, A modem four-circle diffractometer is equipped to perform the necessary photographic measurements which a three-circle diffractometer is unable to do. 

Vandier, L. X-Ray Diffraction Laboratory (online), http //www.lcc-toulouse.fr/ lcc/spip.php articlel20 [accessed March 28,2012]. 

A complete single-crystal X-ray structure determination (Section 5.5) provides the cell dimensions, the space group, a list of positional coordinates for the atomic nuclei in the asymmetric unit, and the atomic displacement parameters (ADPs). The experiment is nowadays feasible with a modest investment of equipment money and human time, provided that a suitable crystal is available - often, the bottleneck for the productivity of an X-ray diffraction laboratory is not machine time, but the preparation of good crystal samples. The result is a high resolution picture of the molecular structure and a detailed description of the crystal packing. Through the ADPs, X-ray diffraction also provides some hints at the intra- and intermolecular dynamics. 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

Both ultrasonic and radiographic techniques have shown appHcations which ate useful in determining residual stresses (27,28,33,34). Ultrasonic techniques use the acoustoelastic effect where the ultrasonic wave velocity changes with stress. The x-ray diffraction (xrd) method uses Bragg s law of diffraction of crystallographic planes to experimentally determine the strain in a material. The result is used to calculate the stress. As of this writing, whereas xrd equipment has been developed to where the technique may be conveniently appHed in the field, convenient ultrasonic stress measurement equipment has not. This latter technique has shown an abiHty to differentiate between stress reHeved and nonstress reHeved welds in laboratory experiments. 

X-ray diffraction patterns yield typical 1.2—1.4 nm basal spacings for smectite partially hydrated in an ordinary laboratory atmosphere. Solvating smectite in ethylene glycol expands the spacing to 1.7 nm, and beating to 550°C collapses it to 1.0 nm. Certain micaceous clay minerals from which part of the metallic interlayer cations of the smectites has been stripped or degraded, and replaced by expand similarly. Treatment with strong solutions of... 

Another major difference between the use of X rays and neutrons used as solid state probes is the difference in their penetration depths. This is illustrated by the thickness of materials required to reduce the intensity of a beam by 50%. For an aluminum absorber and wavelengths of about 1.5 A (a common laboratory X-ray wavelength), the figures are 0.02 mm for X rays and 55 mm for neutrons. An obvious consequence of the difference in absorbance is the depth of analysis of bulk materials. X-ray diffraction analysis of materials thicker than 20—50 pm will yield results that are severely surface weighted unless special conditions are employed, whereas internal characteristics of physically large pieces are routinely probed with neutrons. The greater penetration of neutrons also allows one to use thick ancillary devices, such as furnaces or pressure cells, without seriously affecting the quality of diffraction data. Thick-walled devices will absorb most of the X-ray flux, while neutron fluxes hardly will be affected. For this reason, neutron diffraction is better suited than X-ray diffraction for in-situ studies. 

Fig. 7. A typical X-ray diffraction pattern of the Fepr protein fromZJ. vulgaris (Hil-denborough). The pattern was recorded on station 9.6 at the Synchrotron Radiation Source at the CCLRC Daresbury Laboratory using a wavelength 0.87 A and a MAR-Research image-plate detector system with a crystal-to-detector distance of 220 nun. X-ray data clearly extend to a resolution of 1.5 A, or even higher. The crystal system is orthorhombic, spacegroup P2i2i2i with unit cell dimensions, a = 63.87, b = 65.01, c = 153.49 A. The unit cell contains four molecules of 60 kDa moleculEu- weight with a corresponding solvent content of approximately 48%.

A regularly formed crystal of reasonable size (typically >500 pm in each dimension) is required for X-ray diffraction. Samples of pure protein are screened against a matrix of buffers, additives, or precipitants for conditions under which they form crystals. This can require many thousands of trials and has benefited from increased automation over the past five years. Most large crystallographic laboratories now have robotics systems, and the most sophisticated also automate the visualization of the crystallization experiments, to monitor the appearance of crystalline material. Such developments [e.g., Ref. 1] are adding computer visualization and pattern recognition to the informatics requirements. 

Nuclear magnetic resonance (NMR) spectroscopy is, next to X-ray diffraction, the most important method to elucidate molecular structures of small molecules up to large bio macromolecules. It is used as a routine method in every chemical laboratory and it is not the aim of this article to give a comprehensive review about NMR in structural analysis. We will concentrate here on liquid-state applications with respect to drugs or drug-like molecules to emphasize techniques for conformational analysis including recent developments in the field. 

The author acknowledges the assistance of Mr. Israel Engelberg, who performed some of the mechanical tests. The X-ray diffraction data were collected in the laboratory of Professor M. Greenblatt (Department of Chemistry, Rutgers University) by Ms. Aruna Nathan. The author thanks Mr. Chun Li and Mr. Satish Pulapura for their part in the synthesis and characterization of tyrosine derived polymers. 

Lenhert and Hodgkin (15) revealed with X-ray diffraction techniques that 5 -deoxyadenosylcobalamin (Bi2-coenzyme) contained a cobalt-carbon o-bond (Fig. 3). The discovery of this stable Co—C-tr-bond interested coordination chemists, and the search for methods of synthesizing coen-zyme-Bi2 together with analogous alkyl-cobalt corrinoids from Vitamin B12 was started. In short order the partial chemical synthesis of 5 -de-oxyadenosylcobalamin was worked out in Smith s laboratory (22), and the chemical synthesis of methylcobalamin provided a second B 12-coenzyme which was found to be active in methyl-transfer enzymes (23). A general reaction for the synthesis of alkylcorrinoids is shown in Fig. 4. 

A -DNA The Watson-Crick model of DNA is based on the x-ray diffraction patterns of B-DNA. Most DNA is B-DNA however, DNA may take on two other conformations, A-DNA and Z-DNA. These conformations are greatly favored by the base sequence or by bound proteins. When B-DNA is slightly dehydrated in the laboratory, it takes on the A conformation. A-DNA is very similar to B-DNA except that the base pairs are not stacked perpendicular to the helix axis rather, they are tilted because the deoxyribose moiety puckers differently. An A-DNA helix is wider and shorter than the B-DNA helix. 

In the course of his studies of the dyeing process, he became deeply interested in the structure of natural fibers, and most of his efforts were directed toward this new field of research, with the help of able associates, among them R. Brill, M. Dunkel, G. von Susich, and E. Valkd. His investigation of various aspects of the problem utilized physical means (for example, x-ray diffraction, optical properties, and viscosity) and the purely chemical approach. A young scientist, H. Mark, who later became an authority in the field of high polymers, was appointed head of the physical chemistry laboratory. 

In the laboratories of Natta in Milan it was found that the Ziegler catalysts could polymerize (besides ethene) propene, styrene, and several a-olefins to high linear polymers. These polymers appeared crystalline when examined by X-ray diffraction techniques and were able to give oriented fibers. In less than one year since the preparation of the first polymer of propene, Natta was able to communicate, in the meeting of the Accademia dei Lincei of December 1954 in Rome, that a new chapter had been disclosed in the field of macromolecular chemistry, due to the discovery of processes to obtain polymers with an extraordinary regularity in their structure in terms of both chemical constitution and configuration of the successive monomeric units along the chain of each macromolecule. 

XRD and LEED are laboratory techniques, although synchrotrons offer advantages for X-ray diffraction. EXAFS, on the other hand, is usually done at synchrotrons. This, and the fact that EXAFS data analysis is complicated and not always without ambiguity, have inhibited the widespread use of the technique in catalysis. 

X-rays have wavelengths in the angstrom range, are sufficiently energetic to penetrate solids, and are well suited to probe their internal structure. XRD is used to identify bulk phases, to monitor the kinetics of bulk transformations, and to estimate particle sizes. An attractive feature is that the technique can be applied in situ. We will first discuss XRD as done in the laboratory and then discuss newer applications of XRD as are available by using synchrotron radiation. The theory of X-ray diffraction is given in textbooks of solid state physics [1,2] and in specialized books [3-6]. 

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