Atomic thermal parameters

Atomic thermal parameters derived from single-crystal X-ray diffraction, which increase with increasing disorder and defects in the crystal [1]... 

Of great interest to the molecular biologist is the relationship of protein form to function. Recent years have shown that although structural information is necessary, some appreciation of the molecular flexibility and dynamics is essential. Classically this information has been derived from the crystallographic atomic thermal parameters and more recently from molecular dynamics simulations (see for example McCammon 1984) which yield independent atomic trajectories. A diaracteristic feature of protein crystals, however, is that their diffraction patterns extend to quite limited resolution even employing SR. This lack of resolution is especially apparent in medium to large proteins where diffraction data may extend to only 2 A or worse, thus limiting any analysis of the protein conformational flexibility from refined atomic thermal parameters. It is precisely these crystals where flexibility is likely to be important in the protein function. 

As has become clear in previous sections, atomic thermal parameters refined from X-ray or neutron diffraction data contain information on the thermodynamics of a crystal, because they depend on the atom dynamics. However, as diffracted intensities (in kinematic approximation) provide magnitudes of structure factors, but not their phases, so atomic displacement parameters provide the mean amplitudes of atomic motion but not the phase of atomic displacement (i.e., the relative motion of atoms). This means that vibrational frequencies are not directly available from a model where Uij parameters are refined. However, Biirgi demonstrated [111] that such information is in fact available from sets of (7,yS refined on the same molecular crystals at different temperatures. 

In the X-N method, the experimental electron density is determined from the X-ray diffraction data. The free atom electron density is determined by placing theoretical free atom electron densities at the atomic nuclear positions determined by a neutron diffraction experiment on the same crystal structure at the same temperature, albeit with a crystal of larger size. In the X-N method, it is frequently found that the atomic thermal parameters determined by neutron diffraction do not agree with those determined by X-ray diffraction, even though the experiments were carried out under identical conditions. This requires the introduction of an empirical scaling factor between the two sets of data, which is effective but disconcerting. 

Step 11. At this point a computer program refines the atomic parameters of the atoms that were assigned labels. The atomic parameters consist of the three position parameters x,j, and for each atom. Also one or six atomic displacement parameters that describe how the atom is "smeared" (due to thermal motion or disorder) are refined for each atom. The atomic parameters are varied so that the calculated reflection intensities are made to be as nearly equal as possible to the observed intensities. During this process, estimated phase angles are obtained for all of the reflections whose intensities were measured. A new three-dimensional electron density map is calculated using these calculated phase angles and the observed intensities. There is less false detail in this map than in the first map. 

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. 

No. of thermal parameters refined (cluster hetero atoms treated anisotropically) 4,737... 

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 isotropic equivalent thermal parameters are on the whole larger than in the PbTX-1 dimethyl acetal structure or the structure of the natural product. The B values for atoms on the fused ring skeleton range from 4.7 to 12.6 A (mean square amplitudes of 0.059 and 0.16 A ). Curiously, the largest values are associated with C17-C20 of the 9-membered E ring—the ring that adopts two conformations in crystalline PbTX-1. The acyclic atoms do not have appreciably higher thermal parameters, with the exception of hydroxyl 013, which has a B of 22.4 A 2. 

Thermal parameters of conventional independent-atom refinements using BLFLS [8] were applied as starting values for full multipole refinements, which were performed with VALRAY [10]. Both data sets were successfully refined. The results were compared to those published by Kirfel and Eichhom [7], and good agreement was found. 

The least-squares Molly program based on the Hansen-Coppens model [10] was used to determine atomic coordinates, thermal parameters and multipolar density coefficients in scolecite. In the Hansen-Coppens model, the electron density of unit cell is considered as the superposition of the pseudo-atomic densities. The pseudoatom electron density is given by... 

With data averaged in point group m, the first refinements were carried out to estimate the atomic coordinates and anisotropic thermal motion parameters IP s. We have started with the atomic coordinates and equivalent isotropic thermal parameters of Joswig et al. [14] determined by neutron diffraction at room temperature. The high order X-ray data (0.9 < s < 1.28A-1) were used in this case in order not to alter these parameters by the valence electron density contributing to low order structure factors. Hydrogen atoms of the water molecules were refined isotropically with all data and the distance O-H were kept fixed at 0.95 A until the end of the multipolar refinement. The inspection of the residual Fourier maps has revealed anharmonic thermal motion features around the Ca2+ cation. Therefore, the coefficients up to order 6 of the Gram-Charlier expansion [15] were refined for the calcium cation in the scolecite. 

An enormous variety of solvates associated with many different kinds of compounds is reported in the literature. In most cases this aspect of the structure deserved little attention as it had no effect on other properties of the compound under investigation. Suitable examples include a dihydrate of a diphosphabieyclo[3.3.1]nonane derivative 29), benzene and chloroform solvates of crown ether complexes with alkyl-ammonium ions 30 54>, and acetonitrile (Fig. 4) and toluene (Fig. 5) solvates of organo-metallic derivatives of cyclotetraphosphazene 31. In most of these structures the solvent entities are rather loosely held in the lattice (as is reflected in relatively high thermal parameters of the corresponding atoms), and are classified as solvent of crystallization or a space filler 31a). However, if the geometric definition set at the outset is used to describe clathrates as crystalline solids in which guest molecules... 

Crystal data and parameters of the data collection (at -173°, 50 < 20 < 450) are shown in Table I. A data set collected on a parallelopiped of dimensions 0.09 x 0.18 x 0.55 mm yielded the molecular structure with little difficulty using direct methods and Fourier techniques. Full matrix refinement using isotropic thermal parameters converged to R = 0.I7. Attempts to use anisotropic thermal parameters, both with and without an absorption correction, yielded non-positive-definite thermal parameters for over half of the atoms and the residual remained at ca. 0.15. 

The isotropic thermal parameter listed for those atoms refined anisotropically is the isotropic equivalent. 

Assuming isotropic and harmonic vibration, the thermal parameter B becomes the quantity shown in equation 3.6, where u2 is the mean square displacement of the atomic vibration ... 

Carbon and oxygen atom positions were refined with anisotropic thermal parameters. Hydrogen atoms were not located. Figure 3 shows the molecular structure and the atom numbering scheme utilized for the x-ray data presented in the supplementary material for heritiana acetate. Coordinates, bond length, and bond angles for compound III acetate are available as supplementary material. 

For a cubic site, relations between the cumulants and the coefficients of the OPP model have been derived by Kontio and Stevens (1982), and applied to the Al(4) atom in the alloy VA110 4.2 The coordination of Al(4) is illustrated in Fig. 2.4(a), while the potential along [111], derived from the thermal parameter refinement, is shown in Fig. 2.4(b). It is clear from these figures that higher than third-order terms contribute to the potential, because the deviation from the harmonic curve is not exactly antisymmetric with respect to the equilibrium configuration. The potential appears steeper at the higher temperature, which is opposite to what is expected on the basis of the thermal expansion of the solid. 

In addition to the positional and thermal parameters of the atoms, least-squares procedures are used to determine the scale of the data, and parameters such as mosaic spread or particle size, which influence the intensities through multiple-beam effects (Becker and Coppens 1974a, b, 1975). It is not an exaggeration to say that modern crystallography is, to a large extent, made possible by the use of least-squares methods. Similarly, least-squares techniques play a central role in the charge density analysis with the scattering formalisms described in the previous chapter. 

That the positive bias in the scale factors correlates with an increase in thermal parameters is evident from comparison of X-ray and neutron results (Coppens 1968). The apparent increase in thermal parameters of some of the atoms may be interpreted as the response of the spherical-atom model to the existence of overlap density. Because of the positive correlation between the temperature parameters and k, this increase is accompanied by a positive bias in k. 

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