ConFirm distance geometry approach

As already mentioned in Sec. 5.1.1, ConFirm s best mode uses a distance geometry approach to generate initial conformations for a subsequent geometry optimization and energy minimization step. Thus, also the cyclical portions are fully included in the search procedure and are not taken from a library of predefined ring geometries. 

Theory predicts the same effect for any octahedrally co-ordinated crystal structure or co-ordination compound in which the central ion has four unpaired d electrons. This has been confirmed for CrFo, in which the Cr + is isoelectronic with the Mn + ion (Jack and Maitland, 1957). The Cr-F distance is 2.43 A along the z axis, but only 2.01 and 1.98 A along the x and y axes. Clearly it is not possible always to assume spherically symmetrical ions of fixed radii, since the interionic distances depend on the geometry of the occupied orbitals and the direction of approach of the surrounding groups. 

One can expect (see fine print further) that the greater diffusivity of the counter-ion layer as compared to that established in Helmholtz model, would only affect the velocity distribution profile of the displacement of individual fluid layers in the direct vicinity of the solid surface. The experimentally observed velocity of the mutual motion of the phases with respect to each other, v0, determined, as in Helmholtz model, by the potential change significantly (curve 2 approaches the same limiting value as curve 7 ). This is also confirmed by the fact that the distance between the capacitor plates, 8, which is the only parameter defining the geometry of the system in the Helmholtz model, is not present in the final expression.4 The thickness of the ionic atmosphere, k 1, may be used as the parameter closest to the distance 8, i.e. 8=1/k. 

Figure 3 Structural alignments with discrete properties. Methods are based on discrete properties using the DG algorithm (1) or clique-detection (11) as implemented in distance comparisons (DISCO), and Apex-3D. The structure representation, based on discrete properties, resorts to one atomic descriptor (I), usually the atom type, or multiple atomic or site descriptors (II). In the first method (I), the conformational analysis is restricted to the generation of molecular geometries which allow a common arrangement of selected phaimacophoric moieties present in a rigid compound used as template. In the second method (II), the conformational analysis procedure may involve a systematic enumeration of all the possible conformadons for each ligand. The search similarity is directed towards the confirmation of a predefined pharmacophore postulated by the modeler or from some classical SAR in the case of the active analog approach (1), or the automated identification of pharmacophores and bioacdve conformations (II)...

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