Flexibility molecular

The homopolymers of p-hydroxybenzoic acid have such a high value for the that they are somewhat intractable. Useful materials may, however, be made by copolymerising with a view to introducing some molecular flexibility or reducing chain packing or introducing some non-linear links. Commercially important liquid crystal polyesters are discussed in Chapter 25. 

Copolymerisation, with for example vinyl chloride will reduce the regularity and increase the molecular flexibility. The copolymers may thus be processed at temperatures where the decomposition rates are less catastrophic. 

Analytical approaches to understanding the effect of molecular flexibility on orientational order have concentrated on both the isotropic-nematic and the nematic-smectic transition [61, 62] and mean field theory has shown that cholesteric pitch appears not to depend on the flexibility of the molecule [63]. 

Here the vector rj represents the centre of mass position, and D is usually averaged over several time origins to to improve statistics. Values for D can be resolved parallel and perpendicular to the director to give two components (D//, Dj ), and actual values are summarised for a range of studies in Table 3 of [45]. Most studies have found diffusion coefficients in the 10 m s range with the ratio D///Dj between 1.59 and 3.73 for calamitic liquid crystals. Yakovenko and co-workers have carried out a detailed study of the reorientational motion in the molecule PCH5 [101]. Their results show that conformational molecular flexibility plays an important role in the dynamics of the molecule. They also show that cage models can be used to fit the reorientational correlation functions of the molecule. 

Morris G.A., Patel T.R., Picout D.R., Ross-Murphy S.B., Ortega A., Garcia de la Torre J., Harding S.E. 2008. Global hydrodynamic analysis of the molecular flexibility of galactomannans. Carbohydrate Polymers 72, 356-360. 

This increase was ascribed to diminished molecular flexibility on increasing dendrimer size. 

The peculiar features of the three arAR supermolecules were translated into pharmacophore hypotheses by means of Catalyst software (Figure 8.2, unpublished results). Catalyst treats molecular structures as templates placing chemical functions in 3D space to interact with the receptor. Molecular flexibility is taken into account by considering each compound as a collection of conformers representing different areas of the molecules conformational space within a given energy range. 

However, the CIMI/bc descriptors are relatively simplistic as they did not recognize differences between some important atom types (e.g., halogens). Based on the results of ARD approach, the octanol-water partition coefficient (log P), the molecular flexibility (number of rotatable bonds), the PSA, and the number of hydrogen bond donors were the most important descriptors in the model. None of the descriptors were significantly correlated with each other except log P and PSA for which the correlation was not high ( 0.5). The molecular weight was found to be the least significant descriptor in the model. 

Property-based descriptors, lipophilicity, molecular flexibility, PSA, and number of hydrogen-bond donors are the main parameters influencing the BBB permeability of compounds. 

An important extension to rigid-body fitting is the so-called directed tweak technique [105]. Directed tweak allows for an RMS fit, simultaneously considering the molecular flexibility. By the use of local coordinates for the handling of rotatable bonds, it is possible to formulate analytical derivatives of the objective function. With a gradient-based local optimizer flexible RMS fits are obtained extremely fast. However, no torsional preferences may be introduced. Therefore, directed tweak may result in energetically unfavorable conformations. 

In analyzing the conformational properties of carbohydrates, it has often been the practice to consider individual monomer rings to be rigid units, with the only molecular flexibility lying in torsional rotations about the linkage bonds. 

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