Favorable interaction sites

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. 

Consider what happens when a nonoptimal ligand binds to the protein. The binding of this modified ligand is much weaker not because it s not the right size to fit into the protein-binding site, but because the complementary group on the protein loses a favorable interaction with water that is not replaced by an equally favorable interaction with the ligand (Fig. 2-6). 

The problems of the constancy of a and the site of reaction are closely linked. It is very convenient to assume that the charge on the micellar head groups is extensively neutralized by counterions which bind specifically to the micellar surface. In this way micellar stability is associated with a balance between hydrophobic attractions between apolar groups and coulombic repulsions of the ionic head groups which will be reduced by favorable interactions with the counterions in both the Stem and the diffuse Gouy-Chapman layers. It is the behavior of the counterions which is important in considerations of their chemical reactivity. 

The appearance and dominance of this second-order effect can be interpreted through the strong polarization of the acceptor and donor atoms. It should also be noted that a special approach to softness matching [11,19,51] has been adapted in this study. According to this method, which was originally derived from Pearson s HSAB principle, [17] the most favorable interaction between the sites A and B... 

The interaction of positively charged (9+) cytochrome c(III) with PCu(II) has been studied by the same NMR procedures [115]. The results obtained again indicate that there is a favorable interaction at the remote site. The corresponding interaction of PCu(II) with cytochrome f(M, 33,000) is at present more difficult to interpret without knowledge of the cytochrome f structure. 

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