Refinement Squares

Figure 13.4 Tensile strength development during refining (square symbol corresponds to unrefined).

Traditionally, least-squares methods have been used to refine protein crystal structures. In this method, a set of simultaneous equations is set up whose solutions correspond to a minimum of the R factor with respect to each of the atomic coordinates. Least-squares refinement requires an N x N matrix to be inverted, where N is the number of parameters. It is usually necessary to examine an evolving model visually every few cycles of the refinement to check that the structure looks reasonable. During visual examination it may be necessary to alter a model to give a better fit to the electron density and prevent the refinement falling into an incorrect local minimum. X-ray refinement is time consuming, requires substantial human involvement and is a skill which usually takes several years to acquire. 

A few industrial catalysts have simple compositions, but the typical catalyst is a complex composite made up of several components, illustrated schematically in Figure 9 by a catalyst for ethylene oxidation. Often it consists largely of a porous support or carrier, with the catalyticaHy active components dispersed on the support surface. For example, petroleum refining catalysts used for reforming of naphtha have about 1 wt% Pt and Re on the surface of a transition alumina such as y-Al203 that has a surface area of several hundred square meters per gram. The expensive metal is dispersed as minute particles or clusters so that a large fraction of the atoms are exposed at the surface and accessible to reactants (see Catalysts, supported). 

The structure refinement program for disordered carbons, which was recently developed by Shi et al [14,15] is ideally suited to studies of the powder diffraction patterns of graphitic carbons. By performing a least squares fit between the measured diffraction pattern and a theoretical calculation, parameters of the model structure are optimized. For graphitic carbon, the structure is well described by the two-layer model which was carefully described in section 2.1.3. 

Sperry turned his attention to the American Can Company s huge amount of scrap metal remaining after round can tops were pressed from square sheets. He and his colleagues refined American Can s electrolytic detmning process to deal with this scrap so that absolutely pure tin powder resulted. In 1907 and 1908, Speriy was involved m patent interference cases concerning this detiiiiiiiig process. The outcome was that... 

The parameters were then further refined by four successive least-squares procedures, as described by Hughes (1941). Only hk() data were used. The form factor for zinc was taken to be 2-4 times the average of the form factors for magnesium and aluminum. The values of the form factor for zinc used in making the average was corrected for the anomalous dispersion expected for copper Kot radiation. The customary Lorentz, polarization, temperature, and absorption factors were used. A preliminary combined scale, temperature, and absorption factor was evaluated graph-... 

The reliability factor B was 0276 after the first refinement and 0-211 after the fourth refinement. The parameters from the third and fourth refinements differed very little from one another. The final values are given in Table 1. As large systematic errors were introduced in the refinement process by the unavoidable use of very poor atomic form factors, the probable errors in the parameters as obtained in the refinement were considered to be of questionable significance. For this reason they are not given in the table. The average error was, however, estimated to be 0-001 for the positional parameters and 5% for the compositional parameters. The scattering power of the two atoms of type A was given by the least-squares refinement as only 0-8 times that of aluminum (the fraction... 

X-Ray diffraction from single crystals is the most direct and powerful experimental tool available to determine molecular structures and intermolecular interactions at atomic resolution. Monochromatic CuKa radiation of wavelength (X) 1.5418 A is commonly used to collect the X-ray intensities diffracted by the electrons in the crystal. The structure amplitudes, whose squares are the intensities of the reflections, coupled with their appropriate phases, are the basic ingredients to locate atomic positions. Because phases cannot be experimentally recorded, the phase problem has to be resolved by one of the well-known techniques the heavy-atom method, the direct method, anomalous dispersion, and isomorphous replacement.1 Once approximate phases of some strong reflections are obtained, the electron-density maps computed by Fourier summation, which requires both amplitudes and phases, lead to a partial solution of the crystal structure. Phases based on this initial structure can be used to include previously omitted reflections so that in a couple of trials, the entire structure is traced at a high resolution. Difference Fourier maps at this stage are helpful to locate ions and solvent molecules. Subsequent refinement of the crystal structure by well-known least-squares methods ensures reliable atomic coordinates and thermal parameters. 

The structure was refined by block-diagonal least squares in which carbon and oxygen atoms were modeled with isotropic and then anisotropic thermal parameters. Although many of the hydrogen atom positions were available from difference electron density maps, they were all placed in ideal locations. Final refinement with all hydrogen atoms fixed converged at crystallographic residuals of R=0.061 and R =0.075. 

The structure was refined with block diagonal least squares. In cases of pseudo-symmetry, least squares refinement is usually troublesome due to the high correlations between atoms related by false symmetry operations. Because of the poor quality of the data, only those reflections not suffering from the effects of decomposition were used in the refinement. With all non-hydrogen atoms refined with isotropic thermal parameters and hydrogen atoms included at fixed positions, the final R and R values were 0.142 and 0.190, respectively. Refinement with anisotropic thermal parameters resulted in slightly more attractive R values, but the much lower data to parameter ratio did not justify it. 

The difference electron density map following the last cycle of least squares refinement did not show evidence for a simple disorder model to explain the anomalously high B for the hydroxyl oxygen. Attempts to refine residual peaks with partial oxygen occupancies did not significantly improve the agreement index. 

On the other hand, the correction factor by which W r) is altered through this refined treatment, namely, exp[ —(9n/20)(r/r, ) ] from Eq. (16), depends both on n and on r/Vm If the distance of separation of the ends of the chain lies in the vicinity of its root-mean-square value, i.e., if r / then... 

This function depends on many parameters that will be refined using the least squared method. 

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