Conformations, ligand ring substitution

Two conformations of a substituted ethylenediamine chelate ring. The left-hand conformer has the methyl substituent on the chelate ring displaced away from the rest of the molecule (equatorial), whereas the right-hand conformer places it in an axial disposition where it may clash with another axial ligand, which is thus unfavourable. 

The same technique can be used in some cases to obtain accurate estimates of binding free energy differences for a set of ligands of interest [25, 31-34]. The molecule taken as the reference need not be a real molecule. Indeed, the reference molecule could be intermediate between a large set of molecules of interest, so that conformations that are sufficiently representative of them all are sampled in the reference simulation. The justification for this approach is discussed in detail in Chap. 6. To achieve this for a variety of substituted phenols, Liu et al. [25] added dummy atoms to the ring at the sites they wished to substitute. Such dummy atoms can be softer ... 

The kinetics of formation and dissociation of the Ca2+, Sr2+ and Ba2+ complexes of the mono- and di-benzo-substituted forms of 2.2.2, namely (214) and (285), have been studied in water (Bemtgen et al., 1984). The introduction of the benzene rings causes a progressive drop in the formation rates the dissociation rate for the Ca2+ complex remains almost constant while those for the Sr2+ and Ba2+ complexes increase. All complexes undergo first-order, proton-catalyzed dissociation with 0bs — kd + /ch[H+]. The relative degree of acid catalysis increases in the order Ba2+ < Sr2+ < Ca2+ for a given ligand. The ability of the cryptate to achieve a conformation which is accessible to proton attack appears to be inversely proportional to the size of the complexed metal cation in these cases. 

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