Correlated internal motions

Here a simple extension of the master equation method developed for macromolecules in solution [8.4, 8.22] is used to model correlated internal motions in liquid crystals. By explicitly generating all of the possible conformations in a mesogen and weighing these conformers according to their equilibrium probabilities imposed by the nematic mean field [8.12, 8.14], those improbable conformations that were obtained based on the assumption of independent rotations about different C-C bonds may be effectively eliminated. Thus, internal rotations about different axes are considered to be highly correlated. A similar approach has been used to model correlated internal motions in lamellar mesophases of lyotropic liquid crystals [8.20]. All of the studies still retain the simplifying assumption of decoupling internal rotations from the reorientation of the whole molecule. First, the decoupled model of correlated internal motions is considered. 

Chachaty and co-workers [8.20, 8.37, 8.38] were first to describe correlated internal motions in alkyl chains of surfactant molecules that form lyotropic liquid crystals. The last section described an extension of the master equation method of Wittebort and Szabo [8.4] to treat spin relaxation of deuterons on a chain undergoing trans-gauche jump rotations in liquid crystals. This method was also followed by Chachaty et al. to deal with spin relaxation of nuclei in surfactants. However, they assumed that the conformational changes occur by trans-gauche isomerization about one bond at a time. In their spectral density calculations (see Section 8.3.1), they used a transition rate matrix that was constructed from the jump rate Wi, W2, and Ws about each bond. Since W3 is much smaller than Wi and W2, the time scale of internal motions was practically governed by Wi and W2 of each C-C bond. Since... 

This simple relaxation theory becomes invalid, however, if motional anisotropy, or internal motions, or both, are involved. Then, the rotational correlation-time in Eq. 30 is an effective correlation-time, containing contributions from reorientation about the principal axes of the rotational-diffusion tensor. In order to separate these contributions, a physical model to describe the manner by which a molecule tumbles is required. Complete expressions for intramolecular, dipolar relaxation-rates for the three classes of spherical, axially symmetric, and asymmetric top molecules have been evaluated by Werbelow and Grant, in order to incorporate into the relaxation theory the appropriate rotational-diffusion model developed by Woess-ner. Methyl internal motion has been treated in a few instances, by using the equations of Woessner and coworkers to describe internal rotation superimposed on the overall, molecular tumbling. Nevertheless, if motional anisotropy is present, it is wiser not to attempt a quantitative determination of interproton distances from measured, proton relaxation-rates, although semiquantitative conclusions are probably justified by neglecting motional anisotropy, as will be seen in the following Section. 

For folded proteins, relaxation data are commonly interpreted within the framework of the model-free formalism, in which the dynamics are described by an overall rotational correlation time rm, an internal correlation time xe, and an order parameter. S 2 describing the amplitude of the internal motions (Lipari and Szabo, 1982a,b). Model-free analysis is popular because it describes molecular motions in terms of a set of intuitive physical parameters. However, the underlying assumptions of model-free analysis—that the molecule tumbles with a single isotropic correlation time and that internal motions are very much faster than overall tumbling—are of questionable validity for unfolded or partly folded proteins. Nevertheless, qualitative insights into the dynamics of unfolded states can be obtained by model-free analysis (Alexandrescu and Shortle, 1994 Buck etal., 1996 Farrow etal., 1995a). An extension of the model-free analysis to incorporate a spectral density function that assumes a distribution of correlation times on the nanosecond time scale has recently been reported (Buevich et al., 2001 Buevich and Baum, 1999) and better fits the experimental 15N relaxation data for an unfolded protein than does the conventional model-free approach. 

The previous approach is valid as long as the molecular reorientation can be described by a single correlation time. This excludes molecules involving internal motions and/or molecular shapes which cannot, to a first approximation, be assimilated to a sphere. Due to its shape, the molecule shown in Figure 15 cannot evidently fulfil the latter approximation and is illustrative of the potentiality of HOESY experiments as far as carbon-proton distances and the anisotropy of molecular reorientation are concerned.45 58... 

Figure 15 The model molecule used to demonstrate the possibilities of HOESY experiments in terms of carbon-proton distances and reorientational anisotropy. To a first approximation, the molecule is devoid of internal motions and its symmetry determines the principal axis of the rotation-diffusion tensor. Note that H, H,., H,-, H,/ are non-equivalent. The arrows indicate remote correlations.

Up to this point only overall motion of the molecule has been considered, but often there is internal motion, in addition to overall molecular tumbling, which needs to be considered to obtain a correct expression for the spectral density function. Here we apply the model-free approach to treat internal motion where the unique information is specified by a generalized order parameter S, which is a measure of the spatial restriction of internal motion, and the effective correlation time re, which is a measure of the rate of internal motion [7, 8], The model-free approach only holds if internal motion is an order of magnitude (<0.3 ns) faster than overall reorientation and can therefore be separated from overall molecular tumbling. The spectral density has the following simple expression in the model-free formalism ... 

The molecular reorientation is found to be correlated with NH2 internal motions. The non-planar nature of the molecules is shown by both the uncorrected and the vibrationally corrected data. 

Most FPA studies to date on DNA have lacked sufficient time resolution to observe directly the relaxation of the internal correlation functions. Instead, the initial anisotropy r0 is taken as an adjustable parameter. Equations (4.30) show that such a procedure is completely valid for anisotropic diffusors (i.e., (A ft)2 = (dx(t)2)), provided the rapid internal motion of the transition dipole is isotropic. It has not yet been ascertained whether the internal motion actually is isotropic, so this must be assumed.(83) A recent claim(86) that large amplitudes of polar wobble are required to fit both the small amplitude of initial FPA relaxation 87 and the linear dichroism88 has been refuted. 83j... 

Yamakawa and co-workers have formulated a discrete helical wormlike chain model that is mechanically equivalent to that described above for twisting and bending/79111 117) However, their approach to determining the dynamics is very different. They do not utilize the mean local cylindrical symmetry to factorize the terms in r(t) into products of correlation functions for twisting, bending, and internal motions, as in Eq. (4.24). Instead, they... 

In the previous discussion, the electron-nucleus spin system was assumed to be rigidly held within a molecule isotropically rotating in solution. If the molecule cannot be treated as a rigid sphere, its motion is in general anisotropic, and three or five different reorientational correlation times have to be considered 79). Furthermore, it was calculated that free rotation of water protons about the metal ion-oxygen bond decreases the proton relaxation time in aqua ions of about 20% 79). A general treatment for considering the presence of internal motions faster than the reorientational correlation time of the whole molecule is the Lipari Szabo model free treatment 80). Relaxation is calculated as the sum of two terms 8J), of the type... 

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