Conformer model, relaxation times

Equation (23) predicts a dependence of xR on M2. Experimentally, it was found that the relaxation time for flexible polymer chains in dilute solutions obeys a different scaling law, i.e. t M3/2. The Rouse model does not consider excluded volume effects or polymer-solvent interactions, it assumes a Gaussian behavior for the chain conformation even when distorted by the flow. Its domain of validity is therefore limited to modest deformations under 0-conditions. The weakest point, however, was neglecting hydrodynamic interaction which will now be discussed. 

Plotting U as a function of L (or equivalently, to the end-to-end distance r of the modeled coil) permits us to predict the coil stretching behavior at different values of the parameter et, where t is the relaxation time of the dumbbell (Fig. 10). When et < 0.15, the only minimum in the potential curve is at r = 0 and all the dumbbell configurations are in the coil state. As et increases (to 0.20 in the Fig. 10), a second minimum appears which corresponds to a stretched state. Since the potential barrier (AU) between the two minima can be large compared to kBT, coiled molecules require a very long time, to the order of t exp (AU/kBT), to diffuse by Brownian motion over the barrier to the stretched state at any stage, there will be a distribution of long-lived metastable states with different chain conformations. With further increases in et, the second minimum deepens. The barrier decreases then disappears at et = 0.5. At this critical strain rate denoted by ecs, the transition from the coiled to the stretched state should occur instantaneously. 

Fig. 33 Schematic illustration of the model of two-stage melt relaxation. When ECSCs are melted, the chains within ECSCs are rapidly changed to a random coiled conformation. Then, chains are gradually entangled with each other. Cross-mark denotes the entanglement. rconf and tent are the conformational and topological relaxation time, respectively. At is the melt annealing time (see text)...

Two major models are typically used to describe these situations the concerted model and the sequential model. In the concerted model, the enzyme has two major conformations a relaxed form that can bind the appropriate reactant molecule(s) and a tight form that is unable to tightly bind the reactant molecule(s). In this model, all subunits containing reactive sites change at the same time (Figure 16.7). An equilibrium exists between the active and inactive structures. Binding at one of the sites shifts the equilibrium to favor the active relaxed form. 

For higher modes, the ratio xjxt becomes sensitive to the correlations. As p increases, tp/t, decreases, as shown by Eq. (38). For illustration, this ratio is plotted semilogarithmically in Figure 2 as a function of pjN for a chain with 104 beads and for P = 0, 0.2,0.5, and 0.9. It is seen that in this one-dimensional model the relaxation spectrum is broadened as the energetic preference for extended conformations (P > 0) is increased. In particular, the longest and shortest relaxation times are related by... 

Indeed, 13C spin-lattice relaxation times can also reflect conformational changes of a protein, i.e. helix to random coil transitions. This was demonstrated with models of polyamino acids [178-180], in which definite conformations can be generated, e.g. by addition of chemicals or by changes in temperature. Thus effective molecular correlation times tc determined from spin-lattice relaxation times and the NOE factors were 24-32 ns/rad for the a carbons of poly-(/f-benzyl L-glutamate) in the more rigid helical form and about 0.8 ms/rad for the more flexible random coil form [180],... 

Fig. 2. Temperature dependence of the storage modulus G, loss modulus G", relaxation time t and ratio (n2/nj) of the equilibrium numbers of conformers for a single relaxation time model...

It is instructive to compare the system of equations (3.46) and (3.47) with the system (3.37). One can see that both the radius of the tube and the positions of the particles in the Doi-Edwards model are, in fact, mean quantities from the point of view of a model of underlying stochastic motion described by equations (3.37). The intermediate length emerges at analysis of system (3.37) and can be expressed through the other parameters of the theory (see details in Chapter 5). The mean value of position of the particles can be also calculated to get a complete justification of the above model. The direct introduction of the mean quantities to describe dynamics of macromolecule led to an oversimplified, mechanistic model, which, nevertheless, allows one to make correct estimates of conformational relaxation times and coefficient of diffusion of a macromolecule in strongly entangled systems (see Sections 4.2.2 and 5.1.2). However, attempts to use this model to formulate the theory of viscoelasticity of entangled systems encounted some difficulties (for details, see Section 6.4, especially the footnote on p. 133) and were unsuccessful. 

Derived from linear approximation of the equations (3.37), the equilibrium correlation function (4.29), defines two conformation relaxation times r+ and r for every mode. The largest relaxation times have appeared to be unrealistically large for strongly entangled systems, which is connected with absence of effect of local anisotropy of mobility. To improve the situation, one can use the complete set of equations (3.37) with local anisotropy of mobility. It is convenient, first, to obtain asymptotic (for the systems of long macromolecules) estimates of relaxation times, using the reptation-tube model. 

Computational methods have been applied to study the conformations of free and metal-complexed oxathiacrown ethers 1-4 shown in Figure 6. The results were compared to variable temperature NMR and i spin-lattice relaxation time measurements <2001JP2988>. Theoretical studies included simulated 111 NMR spectra using PERCH and molecular modeling with PM3 semi-empirical quantum-chemical calculations. The NMR and the computational data both show that Ag+ coordinates equally well to S and O atoms, Bi3+ and Sb3+ prefer O atoms, and that Ptz+ and Pdz+ prefer exo-cyclic coordination only to the S atoms in this maleonitrile macrocycle. 

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