Vibration, positional disorder temperature

Notice, however, that the preceding analysis gives only an upper limit and an average, or rms value, of position errors, and further, that the errors result from the limits of accuracy in the data. There are also two important physical (as opposed to statistical) reasons for uncertainty in atom positions thermal motion and disorder. Thermal motion refers to vibration of an atom about its rest position. Disorder refers to atoms or groups of atoms that do not occupy the same position in every unit cell, in every asymmetric unit, or in every molecule within an asymmetric unit. The temperature factor Bj obtained during refinement reflects both the thermal motion and the disorder of atom j, making it difficult to sort out these two sources of uncertainty. 

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. 

The atomic temperature factor, or B factor, measures the dynamic disorder caused by the temperature-dependent vibration of the atom, as well as the static disorder resulting from subtle structural differences in different unit cells throughout the crystal. For a B factor of 15 A2, displacement of an atom from its equilibrium position is approximately 0.44 A, and it is as much as 0.87 A for a B factor of 60 A2. It is very important to inspect the B factors during any structural analysis a B factor of less than 30 A2 for a particular atom usually indicates confidence in its atomic position, but a B factor of higher than 60 A2 likely indicates that the atom is disordered. 

In addition to the dynamic disorder caused by temperature-dependent vibration of atoms, protein crystals have static disorder due to the fact that molecules, or parts of molecules, do not occupy exactly the same position or do not have exactly the same orientation in the crystal unit cell. However, unless data are collected at different temperatures, one cannot distinguish between dynamic and static disorder. Because of protein crystal disorder, the diffraction pattern fades away at some diffraction angle 0max. The corresponding lattice distance <7mm is determined by Bragg s law as shown in equation 3.7 ... 

Atoms are not rigidly bound to the lattice, but vibrate around their equilibrium positions. If we were able to look at the crystal with a very short observation time, we would see a slightly disordered lattice. Incident electrons see these deviations, and this, for example, is the reason that in LEED the spot intensities of diffracted beams depend on temperature at high temperatures the atoms deviate more from their equilibrium position than at low temperatures, and a considerable number of atoms are not at the equilibrium position necessary for diffraction. Thus, spot intensities are low and the diffuse background high. Similar considerations apply in other scattering techniques, as well as in EXAFS and in Mossbauer spectroscopy. 

This intermolecular potential for ADN ionic crystal has further been developed to describe the lowest phase of ammonium nitrate (phase V) [150]. The intermolecular potential contains similar potential terms as for the ADN crystal. This potential was extended to include intramolecular potential terms for bond stretches, bond bending and torsional motions. The corresponding set of force constants used in the intramolecular part of the potential was parameterized based on the ab initio calculated vibrational frequencies of the isolated ammonium and nitrate ions. The temperature dependence of the structural parameters indicate that experimental unit cell dimensions can be well reproduced, with little translational and rotational disorder of the ions in the crystal over the temperature range 4.2-250 K. Moreover, the anisotropic expansion of the lattice dimensions, predominantly along a and b axes were also found in agreement with experimental data. These were interpreted as being due to the out-of-plane motions of the nitrate ions which are positions perpendicular on both these axes. 

The calculation of the structure factor in equation (8) assumes all atoms to be at rest in the positions corresponding to perfect crystal symmetry. In fact, atoms and molecules perform thermal vibrations and sometimes are statically disordered, that is, shifted from ideal positions, differently in different unit cells. Both effects disturb the long-range periodicity of a crystal and thus make it a poorer diffractor. Smearing of the electron distribution of an atom due to thermal vibration effectively reduces its scattering factor fj, so that it drops faster with sin 9IX than the corresponding curve for a stationary atom (/o), as shown in Figure 7. The decrease is described by an exponential temperature, or thermal, factor Q ... 

Because the diffraction experiment involves the average of a very large number of unit cells (of the order of 10 in a crystal used for X-ray diffraction analysis), minor static displacements of atoms closely simulate the effects of vibrations on the scattering power of the average atom. In addition, if an atom moves from one disordered position to another, it will be frozen in time during the X-ray diffraction experiment. This means that atomic motion and spatial disorder are difficult to separate from each other by simple experimental measurements of intensity falloff as a function of sm6/X. For this reason, atomic displacement parameter is considered a more suitable term than the terms that have been used historically, such as temperature factor, thermal parameter, or vibration parameter for each of the correction factors included in the structure factor equation. A displacement parameter may be isotropic (with equal displacements in all directions) or anisotropic (with different values in different directions in the crystal). 

In order to determine whether a decrease in scattering at high angles is due to vibration effects or to disorder, the data should be measured at a series of temperatures. Only the vibration effects should show a strong temperature dependence. Displacements of atoms from their equilibrium positions can be anisotropic and are represented by anisotropic displacement parameters which, are refined by least-squares techniques together with the atomic coordinates (see Chapter 10). A further analysis of these anisotropic displacement parameters in terms of translation T, libration L, and screw S motions can give information on the nature of the molecular motion. 

Temperature factor An exponential expression by which the scattering of an atom is reduced as a consequence of vibration (or a simulated vibration resulting from static disorder). For isotropic motion the exponential factor is exp(—5iso sin 0/A ), where Biso is the isotropic temperature factor. It equals 87r (ti ), where (ti ) is the mean-square displacement of the atom from its equilibrium position. For anisotropic motion the exponential expression usually contains six parameters, the anisotropic vibration or displacement parameters, which describe ellipsoidal rather than isotropic (spherically symmetrical) motion or average static displacements. 

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