Spectral density dynamics

Table Bl.13.1 Selected dynamic models used to calculate spectral densities.

Since the stochastic Langevin force mimics collisions among solvent molecules and the biomolecule (the solute), the characteristic vibrational frequencies of a molecule in vacuum are dampened. In particular, the low-frequency vibrational modes are overdamped, and various correlation functions are smoothed (see Case [35] for a review and further references). The magnitude of such disturbances with respect to Newtonian behavior depends on 7, as can be seen from Fig. 8 showing computed spectral densities of the protein BPTI for three 7 values. Overall, this effect can certainly alter the dynamics of a system, and it remains to study these consequences in connection with biomolecular dynamics. 

Among the dynamical properties the ones most frequently studied are the lateral diffusion coefficient for water motion parallel to the interface, re-orientational motion near the interface, and the residence time of water molecules near the interface. Occasionally the single particle dynamics is further analyzed on the basis of the spectral densities of motion. Benjamin studied the dynamics of ion transfer across liquid/liquid interfaces and calculated the parameters of a kinetic model for these processes [10]. Reaction rate constants for electron transfer reactions were also derived for electron transfer reactions [11-19]. More recently, systematic studies were performed concerning water and ion transport through cylindrical pores [20-24] and water mobility in disordered polymers [25,26]. 

Another way to describe deviations from the simple BPP spectral density is the so-called model-free approach of Lipari and Szabo [10]. This takes account of the reduction of the spectral density usually observed in NMR relaxation experiments. Although the model-free approach was first applied mainly to the interpretation of relaxation data of macromolecules, it is now also used for fast internal dynamics of small and middle-sized molecules. For very fast internal motions the spectral density is given by ... 

The measurement of correlation times in molten salts and ionic liquids has recently been reviewed [11] (for more recent references refer to Carper et al. [12]). We have measured the spin-lattice relaxation rates l/Tj and nuclear Overhauser factors p in temperature ranges in and outside the extreme narrowing region for the neat ionic liquid [BMIM][PFg], in order to observe the temperature dependence of the spectral density. Subsequently, the models for the description of the reorientation-al dynamics introduced in the theoretical section (Section 4.5.3) were fitted to the experimental relaxation data. The nuclei of the aliphatic chains can be assumed to relax only through the dipolar mechanism. This is in contrast to the aromatic nuclei, which can also relax to some extent through the chemical-shift anisotropy mechanism. The latter mechanism has to be taken into account to fit the models to the experimental relaxation data (cf [1] or [3] for more details). Preliminary results are shown in Figures 4.5-1 and 4.5-2, together with the curves for the fitted functions. 

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. 

In Equation (5), we can first notice (i) the factor 1/r6 which makes the spectral density very sensitive to the interatomic distance, and (ii) the dynamical part which is the Fourier transform of a correlation function involving the Legendre polynomial. We shall denote this Fourier transform by (co) (we shall dub this quantity "normalized spectral density"). For calculating the relevant longitudinal relaxation rate, one has to take into account the transition probabilities in the energy diagram of a two-spin system. In the expression below, the first term corresponds to the double quantum (DQ) transition, the second term to single quantum (IQ) transitions and the third term to the zero quantum (ZQ) transition. 

As seen from the above theoretical developments, accessing geometrical (and stereochemical) information implies at least an estimation of the dynamical part of the various relaxation parameters. The latter is represented by spectral densities which rest on the calculation of the Fourier transform of auto- or cross-correlation functions. These calculations require necessarily a model for describing molecular reorientation... 

Elastomers are solids, even if they are soft. Their atoms have distinct mean positions, which enables one to use the well-established theory of solids to make some statements about their properties in the linear portion of the stress-strain relation. For example, in the theory of solids the Debye or macroscopic theory is made compatible with lattice dynamics by equating the spectral density of states calculated from either theory in the long wavelength limit. The relation between the two macroscopic parameters, Young s modulus and Poisson s ratio, and the microscopic parameters, atomic mass and force constant, is established by this procedure. The only differences between this theory and the one which may be applied to elastomers is that (i) the elastomer does not have crystallographic symmetry, and (ii) dissipation terms must be included in the equations of motion. 

The linear response theory [50,51] provides us with an adequate framework in order to study the dynamics of the hydrogen bond because it allows us to account for relaxational mechanisms. If one assumes that the time-dependent electrical field is weak, such that its interaction with the stretching vibration X-H Y may be treated perturbatively to first order, linearly with respect to the electrical field, then the IR spectral density may be obtained by the Fourier transform of the autocorrelation function G(t) of the dipole moment operator of the X-H bond ... 

Owing to the above remarks, it is clear that the spectral densities resulting from the dynamical study of the two-level system, involving relaxational mechanisms, should not be viewed as the simple broadening of the infrared transitions obtained in the undamped frame. 

Equations (1-3) are widely used for protein dynamics analysis from relaxation measurements. The primary goals here are (A) to measure the spectral densities J(co) and, most important, (B) to translate them into an adequate picture of protein dynamics. The latter goal requires adequate theoretical models of motion that could be obtained from comparison with molecular dynamics simulations (see for example Ref. [23]). However, accurate analysis of experimental data is an essential prerequisite for such a comparison. 

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]). 

Spohr found a significant reduction in the dipole reorientation time for a different model of water (but using the same water/Pt potential). In that paper, the reorientation dynamics are characterized by the spectral densities for rotation around the three principal axes of the water molecule. These calculations demonstrated the hindered rotation of water molecules in the plane parallel to the surface. In addition, a reduction in the frequency of rotation about the molecular dipole for water molecules in the adsorbed... 

The strategy, usually adopted to achieve a theoretical description of this complex dynamics, is to describe the influence of the solvent environment on the electron-transfer reaction within linear response theory [5, 26, 196, 197] as linear coupling to a bath of harmonic oscillators. Within this model, all properties of the bath enter through a single function called the spectral density [5, 168]... 

If this observation corresponds to the true situation in solution then the internal motions are an order of magnitude faster than the rotational correlation time. Under such circumstances, the spectral density function used in these calculations is incorrect. This aspect requires further investigation, particularly once the data from dynamics calculations specifically including water become available. 

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