Structural Tools

Lee P A, Citrin P H, Eisenberger P and Kincaid B M 1981 Extended x-ray absorption fine structure—its strengths and limitations as a structural tool Rev. Mod. Rhys. 53 769-806... 

Work on EXAFS then progressed very little until the advent of the synchrotron radiation source (storage ring), described in Section 8.1.1.1. This type of source produces X-ray radiation of the order of 10 to 10 times as intense as that of a conventional source and is continuously tunable. These properties led to the establishment of EXAFS as an important structural tool for solid materials. 

EXAFS is a nondestructive, element-specific spectroscopic technique with application to all elements from lithium to uranium. It is employed as a direct probe of the atomic environment of an X-ray absorbing element and provides chemical bonding information. Although EXAFS is primarily used to determine the local structure of bulk solids (e.g., crystalline and amorphous materials), solid surfaces, and interfaces, its use is not limited to the solid state. As a structural tool, EXAFS complements the familiar X-ray diffraction technique, which is applicable only to crystalline solids. EXAFS provides an atomic-scale perspective about the X-ray absorbing element in terms of the numbers, types, and interatomic distances of neighboring atoms. 

Structural Imperfections. In many respects HREM has had a greater impact upon our knowledge of the nature of the atomic reorganization at crystalline imperfections than any other single technique. One of the very first contributions of HREM as a new analytical and structural tool was described in the paper by Iijimia (42) in 1971 on 2 10 29 v -ewe< down to its b - axis. Structural faults, arising from subtle fluctuations in composition, could be clearly seen in the block-structure (based on NbO octahedra) which is a feature of this ternary oxide system. More than a decade later similar materials are yielding to active scrutiny by HREM, and Horiuchi (43), for example, has shown how point defects may be directly viewed... 

In addition to traditional X-ray techniques to study silk (Bram etal., 1997 Lotz and Cesari, 1979 Riekel et al., 1999a Warwicker, 1960), other structural tools have helped unravel various aspects of silk protein conformation. These include solid-state NMR (Asakura et al., 1983, 1988, 1994 Beek et al., 2000, 2002) studies of native and regenerated silk together with and studies of isotopically edited silks, which have dramatically improved the model of structure distribution within silk fibers (Beek et al., 2000, 2002). 

Ab initio computations have so far proved to be reliable structural tools for neutral carboranes and their anions. They have been used to predict the carborane geometries for six-vertex, eight-vertex, and 11-vertex nido-carboranes,67-69 and for 5-12 vertex r/aro-carboranes.70,71 However, carborane anions in the presence of a group I metal cation may form ion-pair anions with one cation tightly bound to the carborane anion (see Chapter 3.03).72,73 Even computations on a salt with a carborane anion in a non-coordinating solvent would need to include the cation for computed shifts that tally with observed NMR data.74... 

XAS has been successfully employed in the characterization of a number of catalysts used in low temperature fuel cells. Analysis of the XANES region has enabled determination of the oxidation state of metal atoms in the catalyst or, in the case of Pt, the d band vacancy per atom, while analysis of the EXAFS has proved to be a valuable structural tool. However, the principal advantage of XAS is that it can be used in situ, in a flooded half-cell or true fuel cell environment. While the number of publications has been limited thus far, the increased availability of synchrotron radiation sources, improvements in beam lines brought about by the development of third generation sources, and the development of more readily used analysis software should increase the accessibility of the method. It is hoped that this review will enable the nonexpert to understand both the power and limitations of XAS in characterizing fuel cell electrocatalysts. 

Few structural tools are available to assess the structure of crosslinked networks directly. A frequent approach is to derive such information from kinetic study of unreacted monomer during the polymerization process (4). The possibilities for deriving structural information by characterizing network fragments has not been fully explored. 

Structural information on the atomic arrangements at the early stage of formation of metal-metal, metal-semiconductor interfaces and semiconductor-semiconductor heterojunctions is needed along with the determination of the structure of the electron states in order to put on a complete experimental ground the discussion of the formation of solid-solid junctions. Amongst the structural tools that have been applied to the interface formation problem Surface-EXAFS is probably the best... 

In order to obtain detailed structure, a knowledge of diffraction intensities is essential, the intensities being related to the structure factor. Computer-controlled single-crystal X-ray diffractometers with structure (software) packages have made structure elucidation a routine matter. The availability of synchrotron X-radiation of continuously variable wavelength has made X-ray diffraction a still more powerful structural tool for the study of solids. A technique of great utility to solid state chemists is the Rietveld treatment of powder X-ray diffraction profiles (Rietveld, 1969 Manohar, 1983). Automated structure packages for the determination of unknown structures by this method are now commercially available (see section 2.2.3). In Fig. 2.1, we show a typical set of profile data. 

In 3-substituted thiophenes these absorptions are found in the ranges 1555-1481, 1443-1392, 1374-1355 and 1235-1193 cm-1 and the hydrogen in-plane absorption is found in the range 1098-1070 cm-1 (63JCS3881), It is not too likely that one would use IR data as a definitive structural tool in view of the more revealing structural information available from H and 13C NMR spectroscopy. 

Nageswara Rao, B. D., and Kemple, M. D., eds. (1996) NMR as a structural tool for macromolecules Current status andfiiture directions, Plenum, New York... 

Another useful structure tool is RasMol (or RasMac). This will allow you to view the detailed structure of a protein and rotate it on coordinates so you can see it from all perspectives. A hyperlink to RasMol is present under the View Structure function just above Chime. You may need to study RasMol instructions provided under Help, or you may use a Ra.s Mol tutorial listed in Table El.2. Another useful protein viewer is tin-Swiss-Protein Pdv Viewer (Table El.2). BLAST is an advanced sequence similarity tool available at NCBI. To access this, go to the NCBI home page (www.ncbi.nlm.nih.gov) and click on BLAST. Then click on Basic BLAST search to obtain a dialogue box into which you may type the amino acid sequence of human a-lactalbumin. This process may be stream lined by downloading the amino acid sequence in FASTA format into a file and transferring the fde into the BLAST dialogue box. BLAST will provide a list of proteins with sequences similar to the one entered. 

---