Local geometry effects

The calcium sites in troponin C have been studied by X-ray absorption near edge structure (XANES).244 In all four cases, Ca2+ appears to be coordinated to carboxylate and carbonyl groups, and no structural differences could be found between the two classes of sites. Binding of Mg2+ causes a distortion of the geometry of the calcium site. Thus, the reduced affinity for Ca2+ of the Ca2+-Mg2+ sites in the presence of Mg2+ may not simply be due to competition with Mg2+, but due to some conformational change induced at these sites by Mg2+. The similarity of all four Ca2+ sites means that local bonding effects do not explain the inability of Mg2+ to bind to the calcium-specific sites I and II. The XANES of parvalbumin differs from that of troponin C. 

Having resolved the molecular perception problem and achieved a unique representation of all atoms, bonds, and rings in the molecule, the second major step is the definition of the most useful measure for local similarity of atoms and atomic environment. For the purpose of COSMO/rag, we need to achieve the state that atoms are considered as most similar, if their partial molecular surfaces and surface polarities, i.e., polarization charge densities, are most similar. But since the latter is not known, at least for the new molecule under consideration, we have to ensure that the local geometries and the electronic effects of the surrounding atoms are most similar. Obviously, two similar atoms should at legist be identical with respect to their element and their hybridization. Turning this information into a unique real number, a similarity index of the lowest order (zeroth order) can be defined for each atom from the atom element numbers and... 

The Effect of Solvent in Local Geometry (Bonds and Angles)... 

While the effect of solvent in local geometry can be reasonably captured by minimization protocols implemented in most continuum models, the effect of solvent in conformation and in intermolecular geometry requires more powerful methods, since the conformational space of the solute(s) needs to be sample to explore regions which might be quite different from those important in the gas phase. This means that solvation methods need to be... 

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