Extended model-free formalism

In the extended model-free formalism, two internal motions on two separable time scales are taken into account [10] ... 

Meiler et al applied the model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. Ishima et aO compared the methyl rotation axis order parameters derived from the model-free analyses of the and longitudinal and transverse relaxation rates measured in the same protein sample. Best et al reported the results of molecular dynamics simulations compared with NMR relaxation experiments for maltose and isomaltose. Using the model-free formalism they could estimate reliable order parameters. Baber et used an extended model-... 

This model can also be extended to further levels of librational motion, each with its own order parameter and correlation time, and has been underpinned more formally in the three-r case of two librational levels plus rotation [7]. It is clearly of a general nature. One may indeed choose to abandon relationship (4.23) and to re-interpret in (4.24) as a more general order parameter. One thereby achieves a model-free theory, which has advantages over alternative, more specific models for polymer motion (see chapter 6), when the motional details are not clear. 

The titration coordinates evolve along with the dynamics of the conformational degrees of freedom, r, in simulations with GB implicit solvent models [37, 57], An extended Hamiltonian formalism, in analogy to the A dynamics technique developed for free energy calculations [50], is used to propagate the titration coordinates. The deprotonated and protonated states are those, for which the A value is approximately 1 or 0 (end-point states), respectively. Thus, in contrast to the acidostat method, where A represents the extent of deprotonation, is estimated from the relative occupancy of the states with A 1 (see later discussions). The extended Hamiltonian in the CPHMD method is a sum of the following terms [42],... 

The form of the free energy functional G appearing in the Polarizable Continuum Model is discussed in refs [35-37], Recently, Mennucci and Cammi have extended their integral equation formalism model for medium effects on shielding to the NMR shielding tensor for solutions in liquid crystals [38,39],... 

Clemenger s model is, however, non-selfconsistent. Ekardt and Penzar [41,4.3] have extended the jellium mode to account for spheroidal deformations. In this model the ionic background is represented by a distribution of positive charge with constant density and a distorted, spheroidal, shape. The advantage with respect to Clemenger s model is that the spheroidal jellium model is parameter-free and that the calculation of the electronic wave functions is performed self-consistently using the density functional formalism. The distortion parameter is determined by solving the Kohn-Sham equations for different... 

It is here important to reeall that such improvements are not limited to BE solvation methods for example, Rivail and the Nancy group have recently extended their multipole-expansion formalism to permit the analytic computation of first and second derivatives of the solvation free energy for arbitrary cavity shapes, thereby facilitating the assignment of stationary points on a solvated potential energy surface. Analytic gradients for SMx models at ab initio theory have been recently described (even if they have been available longer at the semiempirical level ), and they have been presented also for finite difference solutions of the Poisson equation and for finite element solutions. 

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