Interatomic distances, EXAFS spectra

Therefore, XAS—especially with respect to EXAFS—has many advantages as a probe of transition metal centers in biological materials. Beyond the absence of a requirement for crystalline materials, the major attractions are the specificity, and sensitivity of the technique and the provision of interatomic distances with an accuracy of 0.02 A within (say) 4 A of the primary absorber. However, it should be noted that (1) no angular information is usually obtained (2) rarely does the structural information extend beyond 4 A, (3) the spectrum sums data for all atoms of a particular element and, if the element of interest is present in more than one chemical form, an average environment is obtained (4) the possibility of radiation damage must be anticipated and the integrity of samples should be monitored after, and if possible... 

The EXAFS on Y-edge is very well fitted by a two shell model 3.3 Cu at 2.83 A and 1.5 Cu at 3.03 A. But, in this second shell, the coordination number is extremely ambiguous as it can be raised to 6 by changing the Debye-Waller factor from 0.1 A to 0.15 A. The study of the X-ray scattering data allows to solve this problem. The fitting of the radial distribution functions gives evidence of Cu—Cu interactions. And, finally, the only model which leads to a good reconstruction of the X-ray RDF and of the EXAFS spectrum implies four different subshells, two of them for Cu—Cu correlations and the other ones for Cu—Y correlations. Interatomic distances and coordination numbers appear in Table 7. 

EXAFS confirmed that unpyrolyzed ClFeTMPP adsorbed intact on Vulcan and was still intact up to 325°C. After pyrolysis at 700°C (the optimum temperature for catalytic activity) the first shell of atoms around the Fe ion was still Fe-N4, but the interatomic distance contracted and the Fe ion was now in the N4 plane (Fe ion was above that plane for the intact molecule). The Mossbauer spectrum of samples heat treated at 800°C revealed the formation of magnetic iron oxides that could be chemically leached out. The leached material yielded a spectrum similar to that recorded at 700°C and attributed to the Fe-N4 moiety. Van Veen and collaborators proposed a reaction scheme of what they believed happened to the ClFeTMPP chelates upon pyrolysis. This scheme is illustrated in Figure 3.5. However, they warned the reader that, in Figure 3.5, while the overall structure of the iron catalytic site remained close to the original Fe-N4 moiety, there must be substantial local variation in how this unit is attached to the subjacent carbon support. This study is in agreement with an earlier study by McBreen and collaborators", who analyzed 9 wt% CoTMPP and FeTMPP chelates (about 0.7 wt% metal) adsorbed on Vulcan XC-72 and heat treated in inert atmosphere between 600 and 1,000°C. They found that the heat treatment of the macrocycles... 

Fig. 11, alterations in the type of backseattering atom also will alter the phase and the amplitude of the EXAFS spectrum, even when the interatomic distance is fixed. The spectral pattern of the sine wave for a sulfur scatterer and iron absorber is dramatically different from that of oxygen or nitrogen scatterers with an iron absorber. Thus, sulfur as a first shell atom from iron is easily identified, whereas it is not possible to distinguish oxygen from nitrogen. 

As was the case for XANES, here electronic structure calculations including solvent effects are used to draw conclusions on the most probable coordination isomer and from that structure the interatomic bond distances can be directly compared to the computed EXAFS spectra [150-152]. As EXAFS spectroscopy probes the structure of a statistically averaged system, the most appropriate way of comparing theoretical EXAFS data to experimental ones is to use molecular dynamics trajectories to sample the configuration space, select snapshots and finally compute a statistically average spectrum [89,153] with a direct estimate of the mean square relative disorder (MSRD, also called or the EXAFS Debye-Waller term). However, as discussed in Section 11.2.3, the relevance of MD simulations hinges on how accurate intermolecular interactions are, given that these are usually obtained at DFT level (in Car-Parinello MD simulations) or with force-fields (in classical MD simulations). 

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