Localized motions

Atomistically detailed models account for all atoms. The force field contains additive contributions specified in tenns of bond lengtlis, bond angles, torsional angles and possible crosstenns. It also includes non-bonded contributions as tire sum of van der Waals interactions, often described by Lennard-Jones potentials, and Coulomb interactions. Atomistic simulations are successfully used to predict tire transport properties of small molecules in glassy polymers, to calculate elastic moduli and to study plastic defonnation and local motion in quasi-static simulations [fy7, ( ]. The atomistic models are also useful to interiDret scattering data [fyl] and NMR measurements [70] in tenns of local order. 

If the material is perfectly plastic, i.e., if the yield function is independent of k and a, then = 0 and the magnitude of the plastic strain rate cannot be determined from (5.81). Only its direction is determined by the normality condition (5.80), its magnitude being determined by kinematical constraints on the local motion. 

Local motions Ligand docking flexibility Femtoseconds (fs) to picosec-... 

The spectroscopic techniques that have been most frequently used to investigate biomolecular dynamics are those that are commonly available in laboratories, such as nuclear magnetic resonance (NMR), fluorescence, and Mossbauer spectroscopy. In a later chapter the use of NMR, a powerful probe of local motions in macromolecules, is described. Here we examine scattering of X-ray and neutron radiation. Neutrons and X-rays share the property of being found in expensive sources not commonly available in the laboratory. Neutrons are produced by a nuclear reactor or spallation source. X-ray experiments are routinely performed using intense synclirotron radiation, although in favorable cases laboratory sources may also be used. 

Intermetallics also represent an ideal system for study of shock-induced solid state chemical synthesis processes. The materials are technologically important such that a large body of literature on their properties is available. Aluminides are a well known class of intermetallics, and nickel aluminides are of particular interest. Reactants of nickel and aluminum give a mixture with powders of significantly different shock impedances, which should lead to large differential particle velocities at constant pressure. Such localized motion should act to mix the reactants. The mixture also involves a low shock viscosity, deformable material, aluminum, with a harder, high shock viscosity material, nickel, which will not flow as well as the aluminum. 

Turning from chemical exchange to nuclear relaxation time measurements, the field of NMR offers many good examples of chemical information from T, measurements. Recall from Fig. 4-7 that Ti is reciprocally related to Tc, the correlation time, for high-frequency relaxation modes. For small- to medium-size molecules in the liquid phase, T, lies to the left side of the minimum in Fig. 4-7. A larger value of T, is, therefore, associated with a smaller Tc, hence, with a more rapid rate of molecular motion. It is possible to measure Ti for individual carbon atoms in a molecule, and such results provide detailed information on the local motion of atoms or groups of atoms. Levy and Nelson " have reviewed these observations. A few examples are shown here. T, values (in seconds) are noted for individual carbon atoms. 

Glassy state In amorphous plastics, below the Tg, cooperative molecular chain motions are frozen , so that only limited local motions are possible. Material behaves mainly elastically since stress causes only limited bond angle deformations and stretching. Thus, it is hard, rigid, and often brittle. 

Polycarbonate (PC) serves as a convenient example for both, the direct determination of the distribution of correlation times and the close connection of localized motions and mechanical properties. This material shows a pronounced P-relaxation in the glassy state, but the nature of the corresponding motional mechanism was not clear 76 80> before the advent of advanced NMR techniques. Meanwhile it has been shown both from 2H NMR 17) and later from 13C NMRSI) that only the phenyl groups exhibit major mobility, consisting in 180° flips augmented by substantial small angle fluctuations about the same axis, reaching an rms amplitude of 35° at 380 K, for details see Ref. 17). 

Apparently local motions indicating differences in packing are closely related to the mechanical properties of glassy polymers. One of the puzzling features of the P-relaxation in PC as in other glassy polymers 3 6 76 77) is that it often is suppressed if the glass transition temperature is lowered by adding a plasticizer. The material then becomes brittle, which severely limits the applications of such polymers. Such low... 

Figure 1 Schematic representation of the 13C (or 15N) spin-lattice relaxation times (7"i), spin-spin relaxation (T2), and H spin-lattice relaxation time in the rotating frame (Tlp) for the liquid-like and solid-like domains, as a function of the correlation times of local motions. 13C (or 15N) NMR signals from the solid-like domains undergoing incoherent fluctuation motions with the correlation times of 10 4-10 5 s (indicated by the grey colour) could be lost due to failure of attempted peak-narrowing due to interference of frequency with proton decoupling or magic angle spinning.

While the assumption of an isotropic rotational motion is reasonable for low molecular weight chelates, macromolecules have anisotropic rotation involving internal motions. In the Lipari-Szabo approach, two kinds of motion are assumed to affect relaxation a rapid, local motion, which lies in the extreme narrowing limit and a slower, global motion (86,87). Provided they are statistically independent and the global motion is isotropic, the reduced spectral density function can be written as ... 

The association forces between juxtaposed surfactant monomers is physical, not chemical, so the motion of the hydrocarbon tails within a micelle is similar to the local motion in a sample of pure hydrocarbon. 

Starburst (TM) dendrimers with DTPA can contain 170 bound Gd(III) ions and have relaxivities (per bound Gd) up to 6 times that of Gd-DTPA (308). Both global and local motion contribute to the overall rotational correlation time. Attempts have been made to increase the re-laxivity of Gd(III) by optimizing the rotational correlation time via binding of Gd(III) to derivatized polysaccharides (309) and by binding lipophilic complexes to albumin in serum (310). The latter approach has achieved relaxivities as high as 44.2 mM l s1 for derivatized 72 (311). 

There has been extensive effort in recent years to use coordinated experimental and simulation studies of polymer melts to better understand the connection between polymer motion and conformational dynamics. Although no experimental method directly measures conformational dynamics, several experimental probes of molecular motion are spatially local or are sensitive to local motions in polymers. Coordinated simulation and experimental studies of local motion in polymers have been conducted for dielectric relaxation,152-158 dynamic neutron scattering,157,159-164 and NMR spin-lattice relaxation.17,152,165-168 A particularly important outcome of these studies is the improved understanding of the relationship between the probed motions of the polymer chains and the underlying conformational dynamics that leads to observed motions. In the following discussion, we will focus on the... 

T. Kanaya, K. Kaji,andK. Inoue, Macromolecules, 24,1826 (1991). Local Motions of cis-1,4-... 

Recent progress in protein dynamics studies by NMR was greatly facilitated by the invention of the model-free formalism [28, 32]. In this approach, the local dynamics of a protein are characterized by an order parameter, S, measuring the amplitude of local motion on a scale from 0 to 1, and the correlation time of the motion, T oc. The model-free expression for the correlation function of local motion reads... 

This approach yields spectral densities. Although it does not require assumptions about the correlation function and therefore is not subjected to the limitations intrinsic to the model-free approach, obtaining information about protein dynamics by this method is no more straightforward, because it involves a similar problem of the physical (protein-relevant) interpretation of the information encoded in the form of SD, and is complicated by the lack of separation of overall and local motions. To characterize protein dynamics in terms of more palpable parameters, the spectral densities will then have to be analyzed in terms of model-free parameters or specific motional models derived e.g. from molecular dynamics simulations. The SD method can be extremely helpful in situations when no assumption about correlation function of the overall motion can be made (e.g. protein interaction and association, anisotropic overall motion, etc. see e.g. Ref. [39] or, for the determination of the 15N CSA tensor from relaxation data, Ref. [27]). 

The overall tumbling of a protein molecule in solution is the dominant source of NH-bond reorientations with respect to the laboratory frame, and hence is the major contribution to 15N relaxation. Adequate treatment of this motion and its separation from the local motion is therefore critical for accurate analysis of protein dynamics in solution [46]. This task is not trivial because (i) the overall and internal dynamics could be coupled (e. g. in the presence of significant segmental motion), and (ii) the anisotropy of the overall rotational diffusion, reflecting the shape of the molecule, which in general case deviates from a perfect sphere, significantly complicates the analysis. Here we assume that the overall and local motions are independent of each other, and thus we will focus on the effect of the rotational overall anisotropy. 

Equation (10) is exact in the absence of local motion. It provides a good approximation for the protein core residues, characterized by restricted mobility in the protein backbone in this case both J(0) and /(local motion to p in Eq. (10) is canceled out The approach described here is rather general and accommodates both large 1) and small < 1) molecules and mole-... 

D11/Dj, from 1 to 10. Symbols correspond to synthetic experimental data generated assuming overall tumbling with rc = 5 ns and various degrees of anisotropy as indicated. Model-free parameters typical of restricted local backbone dynamics in protein core, S2=0.87, T oc =20 ps, were used to describe the effect of local motions. The H resonance frequency was set to 600 MHz. The solid lines correspond to the right-hand-side expression in Eq. (10). 

Tab. 12.1 Parameters of the models of local motion for the relaxation data ana program DYNAMICS. lysis using computer...

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