Despite recent investigations aimed at modeling 3D QSAR for dye molecules a controversy still exists: can a pharamacophore hypothesis be used for such purposes. In the present publication we reported on the application of the CoMSA method for modeling 3D QSAR of azo and anthraquinone dyes. We obtained very predictive models, which significantly outperform those reported in the previous CoMFA studies, especially for the azo dyes. Our results proved the previous conclusion that steric requirements are far less pronounced for the cellulose cavities than for the classical drug receptor. Moreover, our results indicate that all molecular surface segments are important for dye-fiber interactions, which also makes an important difference in relation to the classical drug pharmacophore. On the other hand, high predictivity of the CoMSA models indicates that a pharmacophore concept is suitable for the description of the dye-fiber interactions. However, this pharmacophore must substantially differ from the drug pharmacophore used for the illustration of the drug-receptor interactions. From a theoretical point of view dye-cellulose interactions can be an interesting case in which shape decides the activity rules not by the steric repulsion but as a cofactor determining the electrostatic potential distribution.

This study describes the interaction between crystalline cellulose and the direct dye Congo red (CR) using molecular dynamics simulations. A model of a microfibril corner of cellulose Ib, exposing one hydrophobic (1 0 0) and the two hydrophilic (1 1 0) and (1 -1 0) surfaces was built. The energetic and geometric features of the dye adsorption were investigated at different temperatures following different initial positions of the CR. The relative positions and orientations of the CR with respect to the cellulose surface were unambiguously characterized using three translation (shift, slide, and rise) and three rotation (roll, tilt, and twist) parameters. Changes of twist and roll parameters showed that there was a tendency for the once adsorbed dye molecules, to become more planar and parallel to the cellulose surface. Several stable adsorption sites, translated laterally with respect to one another were obtained and adsorbed CR molecules were laid with their long axis either parallel or inclined by 50°with respect to the cellulose chain axis. Both vacuum and explicit water environments were considered. In this latter case, there was an increase in the energy of interaction between CR and cellulose and the adsorbed dye molecule behaved more rigidly than in vacuum case.

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