Atom environment

P Koehl, M Delame. Polar and nonpolar atomic environments m the protein core Implication for folding and binding. Pi-otems 20 264-278, 1994. 

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. 

Unlike the energy of an atom, which can be defined in terms of its local atomic environment, its chemical potential is a truly non-local quantity. In thermal equilibrium the chemical potential of each species is a constant throughout the system, whether atoms are at the interface or in the bulk. 

M. C. Desjonqueres and D. Spanjaard, Concepts in Surface Physics, Second Edition, Springer Verlag, Berlin (1996) and references therein R. Haydock, V. Heine and M. J. Kelly, Electronic Structure Based on the Local Atomic Environment for Tight-Binding Bands,. Phys. C 5 2845 (1972)... 

EELS spectra showing the distinction between copper atom environments on the basis of the near edge fine structure of the CuL edge,... 

Ruppe S, A Neumann, E Braekevalt, GT Tomy, GA Stern, KA Maruya, W Vetter (2004) Anaerobic transformation of compounds of technical toxaphene. 2. Fate of compounds lacking geminal chlorine atoms. Environ Toxicol Chem 23 591-598. 

Local surface structure and coordination numbers of neighbouring atoms can be extracted from the analysis of extended X-ray absorption fine structures (EXAFS). The essential feature of the method22 is the excitation of a core-hole by monoenergetic photons modulation of the absorption cross-section with energy above the excitation threshold provides information on the distances between neighbouring atoms. A more surface-sensitive version (SEXAFS) monitors the photoemitted or Auger electrons, where the electron escape depth is small ( 1 nm) and discriminates in favour of surface atoms over those within the bulk solid. Model compounds, where bond distances and atomic environments are known, are required as standards. 

X-ray absorption spectroscopy is a reliable and routine method to investigate the local atomic environments of selected elements in materials, and provides useful... 

Scolecite gave the opportunity to relate the electron density features of Si-O-Si and Si-O-AI bonds to the atomic environment and to the bonding geometry. After the multipolar density refinement against Ag Ka high resolution X-ray diffraction data, a kappa refinement was carried out to derive the atomic net charges in this compound. Several least-squares fit have been tested. The hat matrix method which is presented in this paper, has been particularly efficient in the estimation of reliable atomic net charges in scolecite. 

Although the oxygen atom environment is common in vanadium chemistry54 it is rarely used to support the V- C functionality.55 Two significant exceptions in... 

These difficult experimental controversies show that there is a significant role for NMR, a non-perturbing non-destructive technique that provides structural information about the local atomic environment over several bonds. 

Temperature-programmed reduction combined with x-ray absorption fine-structure (XAFS) spectroscopy provided clear evidence that the doping of Fischer-Tropsch synthesis catalysts with Cu and alkali (e.g., K) promotes the carburization rate relative to the undoped catalyst. Since XAFS provides information about the local atomic environment, it can be a powerful tool to aid in catalyst characterization. While XAFS should probably not be used exclusively to characterize the types of iron carbide present in catalysts, it may be, as this example shows, a useful complement to verify results from Mossbauer spectroscopy and other temperature-programmed methods. The EXAFS results suggest that either the Hagg or s-carbides were formed during the reduction process over the cementite form. There appears to be a correlation between the a-value of the product distribution and the carburization rate. 

Brice, K.A., Derwent, R.G. (1978) Emissions inventory for hydrocarbons in United Kingdom. Atom. Environ. 12, 2045-2054. 

Finizio, A., Mackay, D., Bidleman, T.F., Hamer, T. (1997) Octanol-air partition coefficient as a predictor of partitioning of semivolatile organic chemicals to aerosols. Atoms. Environ. 31(15), 2289-2296. 

Pupp, C., Lao, R.C., Murray, J. J., Pottie, R.F. (1974) Equilibrium vapor concentrations of some polycyclic aromatic hydrocarbons, arsenic trioxide (As4Os) and selenium dioxide, and the collection efficiencies of these air pollutants. Atoms. Environ. 8, 915-925. 

Atomic environment definition (and symbols) and corresponding coordination numbers andpolyhedra... 

As mentioned in the previous paragraphs, to define an atomic environment they used the maximum gap rule. The Brunner-Schwarzenbach method was considered, in which all interatomic distances between an atom and its neighbours are plotted in a histogram such as those shown in Fig. 3.17. The height of the bars is proportional to the number of neighbours, and all distances are expressed as reduced values relative to the shortest distance. In the specific case of CsCl, having a = 411.3 pm,... 

In most cases a clear maximum gap is revealed (here the gap between the second and the third bar). The atomic environment is then constructed with the atoms to the left of this gap (8 + 6 in the example of CsCl). To avoid in particular cases bad or ambiguous descriptions, however, a few additional rules have been considered. When for instance two (or more) nearly equal maximum gaps were observed, a selection was made in order to keep, in a given structure type, the number of different AET as small as possible. A convexity criterion for the environment polyhedron was also considered. The coordination polyhedron has to be defined as the maximum convex volume around only one central atom enclosed by convex faces with all coordinating faces lying at the intersections of at least three faces. This rule was especially used where no clear maximum gap was detectable. 

Daams et al. (1992) have analysed all the cubic structure types reported in Villars and Calvert (1985), after excluding all oxides and a few types with improbable interatomic distances, thus leaving 128 structure types representing 5521 compounds. Their analysis showed that these cubic structure types have 13 917 atomic environments (point sets). Of those environments, 92% belong to one of the 21 most frequently occurring AET, which are those reported in the following list (see also Fig. 3.18) ... 

Figure 3.18a. AET (According to Daams and Villars 1992,1993,1994,1997). The polyhedra corresponding to frequently observed AET are shown together with their codes. The Frank-Kasper (FK) polyhedra are indicated (see 3.9.3.1). Notice the same code 122 2 of the two polyhedra describing the cubic (c) as well as the hexagonal (h) atomic environments of the two ideal close-packed structures.

The results of a similar analysis of the intermetallic hexagonal structure types have been reported by Daams and Villars (1994). Of 442 structure types, 315 (clearly intermetallic and correctly refined) were considered. In this case too it was observed that a small group of atomic environments is greatly preferred. The 23 AET most frequently occurring in the 315 hexagonal structure types are reported in the following list (to be compared with those previously reported for cubic and rhombohedral structure types) ... 

Concluding this section, we may mention a paper by Daams and Villars (1993) concerning an atomic environment classification of the chemical elements. Critically evaluated crystallographic data for all element modifications (and recommended atomic volumes) have been reported. Special structural stability diagrams were used to separate AET stability domains and to predict the structure (in terms of environment types) of hitherto unknown high-pressure and high-temperature modifications. Reference to the use of AET in thermodynamic (CALPHAD) modelling and calculation has been made by Ferro and Cacciamani (2002). 

A summary of this analysis of the atomic environments is shown in Fig. 3.18, where the most common frequently occurring AET are depicted with their symbols and codes. 

As a conclusion to this section it is worth mentioning the atomic environments , defined and coded by Daams et al. (1992). A short description of this topic has been given in 3.7.5 together with some remarks about the classification of AET and their description and coding in terms of coordination polyhedra. 

---