Hydrophobic force field

Mishra, A., PateL S., Behera, R.K., Mishra, B.K., Behera, G.B. Dye-surfactant interaction role of an alkyl chain in the localization of styrylpyridinium dyes in a hydrophobic force field of a cationic surfactant (CTAB). Bull. Chem Soc. Jpn. 1997, 70(12), 2913-2918. 

What are the essential features of surfactant systems An important ingredient is obviously the repulsion between water and nonpolar molecules or molecule parts, the hydrophobic force. This interaction is however highly nontrivial, and its analysis is still an active field of research [4,22,23]. Qualitatively, it is usually attributed to the strong orientational and positional correlations between nonpolar molecules in solution and the surrounding water molecules. The origin of the interaction is therefore entropic free water forms a network of hydrogen bonds. In the neighborhood... 

Supramolecular chemistry takes into consideration the weak and reversible non-covalent interactions between molecules, which include H-bond-ing, metal coordination, hydrophobic forces, van der Waals forces, n—n interactions, and covers different research fields, for example, molecular recognition, host-guest chemistry, mechanically interlocked and nanochemistry. 

The interaction of drug molecules with biological membranes is a three-dimensional (3D) recognition that is mediated by surface properties such as shape, Van der Waals forces, electrostatics, hydrogen bonding, and hydrophobicity. Therefore, the GRID force field [5-7], which is able to calculate energetically favorable interaction sites around a molecule, was selected to produce 3D molecular interaction fields. 

Several review articles have been published on the catalytic functions of micelles and related systems (Fendler and Fendler, 1970, 1975 Menger, 1977 Berezin et al., 1973 Cordes and Dunlap, 1969 Cordes and Gitler, 1973 Kunitake, 1977 Kunitake and Okahata, 1976 Bunton, 1979). The conventional catalytic functions of micelles are, in most cases, related to (i) the concentration of reactants and catalytic acid-base species in the micellar phase due to electrostatic and/or hydrophobic forces and (it) the stabilization of transition states and/or destabilization of initial states by the micellar environments. The situation is more complex when one of the reagents is hydrophilic (Bunton et al., 1979). However, the last few years have witnessed several novel advances in this field especially in relation to enzymatic catalysis. 

Cation-TT interactions are another important motif, dominated by electrostatic interactions [47] within mainly hydrophobic subsites. Such a stabilizing interaction takes place between cations like ammonium ions and electron-rich jt-systems of neighboring aromatic rings. Both interactions are often not explicitly contained in common force fields or scoring functions. 

Cruciani et al., used a dynamic physicochemical interaction model to evaluate the interaction energies between a water probe and the hydrophilic and hydrophobic regions of the solute with the GRID force field. The VolSurf program was used to generate a PLS model able to predict log Poet [51] from the 3D molecular structure. 

Stereo view of the sixty propane minima (thick lines) obtained with the modified force field (see text) on the surface of the A peptide chain (medium lines) of the GCN4 leucine zipper (PDB code 2ZTA). Although the peptide chain was removed during the MCSS procedure, its backbone and hydrophobic side chains are also drawn (thin lines) to show how the propane minima match the aliphatic groups of chain B. Hydrophobic residues are labeled at their Ca atom.Five clusters of propane minima that do not match the hydrophobic side chain of the helix involved in the interhelical interactions are labeled from A (top right) to E (bottom center) and discussed in the text. 

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