Thermal motion/factor

The temperature factor (together with the Cartesian coordinates) is the result of the rcfincincnt procedure as specified by the REMARK 3 record. High values of the temperature factor suggest cither disorder (the corresponding atom occupied different positions in different molecules in the crystal) or thermal motion (vibration). Many visualisation programs (e.g., RasMol [134] and Chime [155]) have a special color scheme designated to show this property. 

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. 

The terms involving the subscript j represents the contribution of atom j to the computed structure factor, where nj is the occupancy, fj is the atomic scattering factor, and Ris the coordinate of atom i. In Eq. (13-4) the thermal effects are treated as anisotropic harmonic vibrational motion and U =< U U. > is the mean-square atomic displacement tensor when the thermal motion is treated as isotropic, Eq. (13-4) reduces to ... 

Small molecule crystallographers are familiar with these concepts, since it is routine to measure data at low temperature to improve precision by reduction of thermal motion, and structures are often done at multiple temperatures to assess the origins of disorder in atomic positions. Albertsson et al. (1979) have reported the analysis of the crystal structure of Z)(-l-)-tartaric acid at 295, 160, 105, and 35 K. Figure 22 shows the individual isotropic. S-factors for the atoms in the structure at each of these temperatures the smooth variation of B with T is apparent. Below 105 K, B is essentially identical for all atoms and is also temperature independent the value of B = 0.7 agrees well with the expected zero-point vibradonal value. However, even for this simple structure, not all of the atoms show B vs T behavior at high temperature which extrapolates to 0 A at 0 K. 

The thermal motion of molecules of a given substance in a solvent medium causes dispersion and migration. If dispersion takes place by intermolecular forces acting within a gas, fluid, or solid, molecular diffusion takes place. In a turbulent medium, the migration of matter within it is defined as turbulent diffusion or eddy diffusion. Diffusional flux J is the product of linear concentration gradient dCldX multiphed by a proportionality factor generally defined as diffusion coefficient (D) (see section 4.11) ... 

Here, ks is the Boltzmann constant (1.38 x 10-23 J/K), T is the absolute temperature (300 K at room temperature), B is the bandwidth of measurement [typically about 1000 Hz for direct current (dc) measurement], /o is the resonant frequency of the cantilever, and Q is the quality factor of the resonance, which is related to damping. It is clear from Eq. (12.8) that lower spring constant, K, produces higher thermal noise. This thermal motion can be used as an excitation technique for resonance frequency mode of operation. 

When observed structure factors are used, the thermally averaged deformation density, often labeled the dynamic deformation density, is obtained. An attractive alternative is to replace the observed structure factors in Eq. (5.8) by those calculated with the multipole model. The resulting dynamic model deformation map is model dependent, but any noise not fitted by the muitipole functions will be eliminated. It is also possible to plot the model density directly using the model functions and the experimental charge density parameters. In that case, thermal motion can be eliminated (subject to the approximations of the thermal motion formalism ), and an image of the static model deformation density is obtained, as discussed further in section 5.2.4. 

As first shown by Dawson (1967), Eq. (11.3) can be generalized by inclusion of anharmonicity of the thermal motion, which becomes pronounced at higher temperatures. We express the anharmonic temperature factor of the diamond-type structure [Chapter 2, Eq. (2.45)] as 71(H) = TC(H) -f iX(H), in analogy with the description of the atomic scattering factors. Incorporation of the temperature... 

It is noteworthy that the zeolites have significantly higher thermal motion than the simpler silicates. The room-temperature equivalent isotopic temperature factors for Si and O in sodium zeolite A are reported as 1.85 and 3.0 A2, respectively, compared with 0.49 and 0.99 A2 in quartz. 

For vanadium, the ratios are smaller, and the dynamic density maps do not show a distinct maximum in the cube direction. The difference is attributed to anharmonicity of the thermal motion. Thermal displacement amplitudes are larger in V than in Cr, as indicated by the values of the isotropic temperature factors, which are 0.007 58 and 0.00407 A2 respectively. As in silicon, the anharmonic displacements are larger in the directions away from the nearest neighbors, and therefore tend to cancel the asphericity of the electron density due to bonding effects. 

Johnson CK (1969) Addition of higher cumulants to the crystallographic structure-factor equation a generalized treatment for thermal-motion effects. Acta Crystallogr A 25 187-194... 

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