Crystal structure solution/refinement

Sheldrick, G. M. SHELXTL-PLUS Program for Crystal Structure Solution and Refinement University of Gottingen Gottingen, Germany, 1997. 

MacLean et al. (2000) have recently smdied the dimorphic behaviour of the pigment precursor ( latent pigment) derivative of 8-VI (R = COOr-but, R = H) (abbreviated DPP-Boc). The latency is due to the thermal decomposition reaction of both polymorphs resulting in the commercially important pigment DPP. The a form of DPP-Boc contains three half molecules in the asymmetric unit (see also Ellern et al. 1994) while the form contains one half molecule per asymmetric unit. Hence, they are easily distinguishable by solid state NMR as well as by X-ray powder diffraction. The crystal structure solution from powder data and Rietveld refinement of both polymorphs is an exemplary smdy demonstrating the potential of these methods in determining the detailed crystal structure of these compounds which are often difficult to crystallize. 

Figure 4.1. The flowchart illustrating common steps employed in a structural characterization of materials by using the powder diffraction method. It always begins with the sample preparation as a starting point, followed by a properly executed experiment both are considered in Chapter 3. Preliminary data processing and profile fitting are discussed in this chapter in addition to common issues related to phase identification and analysis. Unit cell determination, crystal structure solution and refinement are the subjects of Chapters 5,6, and 7, respectively. The flowchart shows the most typical applications for the three types of experiments, although any or all of the data processing steps may be applied to fast, overnight and weekend experiments when justified by their quality and characterization goals.

A crystal structure solution does not end with the development of a plausible model after the model has been built completely, multiple structural and profile parameters should be refined to achieve the best... 

We have seen this powder diffraction pattern several times throughout this text. The histogram collected from the nearly spherical LaNi4.85Sno.15 powder, produced by high pressure gas atomization from a melt, was used to illustrate both the quality of x-ray diffraction data and as one of the examples in the ab initio crystal structure solution. To demonstrate the Rietveld refinement of this crystal structure we will begin with the profile and unit cell parameters determined from Le Bail s algorithm Table 6.3) and the model of the crystal structure determined from sequential Fourier maps as described in section 6.9 and listed in Table 6.8. 

Fully refined original model found during the ab initio crystal structure solution. Table 6.28 3.91 5.20 1.69 2.85... 

A single crystal of kanemite suitable for refinement was found in nature [2], Makatite single crystals were synthesized in the presence of triethanolamine [19,23]. The other M-SHs could not be synthesized with crystals large enough for a single crystal refinement. Based on a methodical approach using an ab initio crystal structure solution, Vortmann et al. [20] solved the structure of RUB-18 from X-ray powder diffraction data. 

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. 

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. 

In a multidomain protein whose domains have fixed orientations relative to each other, a unique alignment tensor will represent the preferred orientation of all the domains in the anisotropic environment. Therefore, structure refinement with dipolar couplings is performed as in one-domain proteins (Sect. 8.4). Several examples are reported in the literature of cases with conformational ambiguity due to the lack of NOE contacts between the domains. One example is the determination of subdomain orientation of the riboso-mal protein S4 z)41 [97]. In this work the lack of NOE contacts between the domains produces an ambiguity in interdomain orientation. The authors use two different anisotropic media to obtain dipolar couplings (DMPC/DHPC bicelles and Pfl filamentous bacteriophages). They conclude that subdomain orientation in solution is similar to the one present in the crystal structure. 

Recent developments and prospects of these methods have been discussed in a chapter by Schneider et al. (2001). It was underlined that these methods are widely applied for the characterization of crystalline materials (phase identification, quantitative analysis, determination of structure imperfections, crystal structure determination and analysis of 3D microstructural properties). Phase identification was traditionally based on a comparison of observed data with interplanar spacings and relative intensities (d and T) listed for crystalline materials. More recent search-match procedures, based on digitized patterns, and Powder Diffraction File (International Centre for Diffraction Data, USA.) containing powder data for hundreds of thousands substances may result in a fast efficient qualitative analysis. The determination of the amounts of different phases present in a multi-component sample (quantitative analysis) is based on the so-called Rietveld method. Procedures for pattern indexing, structure solution and refinement of structure model are based on the same method. 

In conclusion, using high-quality STD-NMR data on UDP-Gal weakly binding to 34 GalTl, we demonstrated that it is possible to refine the crystal structure (or any computer-docked structure in the proper orientation that serves as the starting structure) to obtain a global-minimum conformation for the bound ligand in solution. 

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