Bond reorientation dynamics

Among the various types of local motions that take place in polymer liquids, the change in the orientation of individual bonds with time is one that can be readily evaluated from the molecular dynamics simulations. The bond reorientation motions are also amenaUe to experimental measurement by means of a number of techniques. We investigate the bond reorientation dynamics by evaluating three types of quantities, the distribution W(0,t) of reorientation angle 6 that a bond has undergone during a time interval t, and the time correlation functions... 

Any attempt to explain our result of bond reorientation dynamics on the basis of superposition of rotational diffusion processes encounters a contradiction. If such an explanation was to be valid, the same spectrum of D had to be able to explain the shape of the observed Mi(t) and MaCO functions and the broad nature of the reorientation angle distribution W(6,t) at the same time. The spectrum g(x) of correlation time t or the equivalent spectrum g(D) of the rotational diffusion coefficient D can be evaluated from the correlation functions by means of a numerical procedure such as CONTIN [45]. When the correlation function can be represented by an analytical function, the spectrum can be obtained more conveniently by means of inverse Laplace transformation. In the case of a KWW function, with t and p characterizing the function as given in Eq. (12), g(D) can be calculated by [46]... 

The vibrational dynamics of water solnbilized in lecithin-reversed micelles appears to be practically indistingnishable from those in bulk water i.e., in the micellar core an extensive hydrogen bonded domain is realized, similar, at least from the vibrational point of view, to that occurring in pure water [58], On the other hand, the reorientational dynamics of the water domain are strongly affected, due to water nanoconfmement and interfacial effects [105,106],... 

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. 

In this section we will discuss results of transient IR spectroscopy of different alcohols in solution in a wide concentration range from almost monomeric alcohol samples to strongly associated oligomers. In order to investigate the influence of hydrogen bonds on the dynamical properties of the molecules, we present first a discussion of the data on the vibrational and reorientational dynamics of the OH mode of isolated molecules in the solvent. 

The still faster ( nsec) dynamics of local motions of polymer molecules in dilute solutions have been investigated by Ediger and coworkers (Zhu and Ediger 1995, 1997). They find that the rates of these local motions of a few bonds are not proportional to the solvent viscosity, unless the solvent reorientation rate is fast compared to the polymer local motion. Thus, for local motions (such as bond reorientations) of polymer molecules, Stokes law of drag does not always hold. 

B. Jana, S. Pal, and B. Bagchi, Hydrogen bond breaking mechanism and water reorientational dynamics in the hydration layer of lysozyme. J. Phys. Chem. B, 112 (2008), 9112. 

For the dipolar relaxation mechanism, the spin lattice relaxation time is sensitive to the reorientation dynamics of the CH bond vectors. Different orientations of the CH bond result in slightly different magnetic fields at the carbon nucleus and the modulation of this field allows the spin flips to occur. When we define ecn as the unit vector along a CH bond, the second Legendre polynomial of its autocorrelation function is given by... 

Echodu et al. have studied furanose dynamics in the Hhal methyl-transferase target DNA using solution and solid-state NMR relaxation measurements. In order to interpret previously obtained experimental results quantitatively, a dynamic model of furanose rings based on the analysis of solid-state line shapes has been proposed. The motions were modelled by treating bond reorientations as Brownian excursions within a restoring potential. It was concluded that the local internal motions of this DNA oligomer in solution and in the hydrated solid-state are virtually the same. 

G. Stirnemann, S. Castrillon, J. Hynes, P. Rossky, P. Debenedetti and D. Laage, Non-monotonic dependence of water reorientation dynamics on surface hydrophilicity Competing effects of the hydration structure and hydrogen-bond strength. Phys. Chem. Chem. Phys. 13,19911-19917 (2011). 

As the ion concentration increases, it is not possible to disentangle the effects of cations and of anions on the water reorientation dynamics because of the formation of solvent-shared ion pairs. Nevertheless, van der Postand Bakker [121] showed that sodium ions at concentrations up to 6 m slow down the reorientation of water molecules in aqueous NaCl and Nal, compared with CsCl and KI at the same concentration. Small effects are shown as the concentration of Lil increases up to 2 m, but gradual slowing down of is seen in aqueous Cs SO and Mg(C10 )2 and much more so in aqueous Na SO and MgSO, but the effects diminish as the temperature increases from 22 to 70°C as found by Tielrooij et al. [122]. In 6m NaOH solutions, the reorientation time of the OH hydration complex is r =12 2ps, that is, much slowed down relative to bulk water, because it is a large hydrogen-bonded structure that reorients as a whole according to Liu et al. [123]. 

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