Geometry secondary interactions

A secondary bond , as defined by Alcock [6-8], is an interaction between two atoms characterized by a distance longer than the sum of the covalent radii but shorter than the sum of the van der Waals radii of the corresponding atoms. Such secondary interactions are weaker than normal covalent or dative bonds, but strong enough to connect individual molecules and to modify the coordination geometry of the atoms involved. They are often present in a crystal, thus resulting in self-assembled supermolecules or supramolecular architectures. For gold complexes,... 

Coordination numbers are so dependent on hgand geometry that the concept of preferred coordination number is of limited use. For example, hthium may be said to prefer 4 coordination, but examples of 1 to 12 coordination are known. Low formal coordination numbers are often accompanied by secondary interactions with other sources of electron density, such as C H bonds and arene 7r-systems. There are even examples of C H activation caused by a low-coordinate sodium cation. Of course, there is a trend towards higher preferred coordination for the heavier group members (6 for Na, K 8 for Rb, Cs). 

When phenol, the functional group of the Tyr residue, was paired with water, the optimal geometry was found [154] to contain the expected OH- - -O H-bond. The phenol could serve as either proton donor or acceptor, but in either case, one of the C-H groups of the phenol was in position to form a secondary H-bond as illustrated in Fig. 11. No estimate was made of the energetic contribution of this secondary interaction. 

By far the most studied of Hg(II)-thiolate compounds are those with the stoichiometry Hg(SR)2- While no vibrational studies have been carried out in the vapor phase or in matrix isolation, a number of solution studies exist, and many solid-state vibrational spectra have been reported. In some cases, significant differences in solution and solid-state spectra are found. The vibrational data are consistent with linear coordination in the vast majority of compounds. Where important secondary interactions exist or when the geometry changes from linear to tetrahedral (as in the structurally characterized Hg(S-f-Bu)2, Fig. 7), the Raman and IR data reflect deviation from simple linear coordination, although in some cases, the proper assignment of Hg-S vibrational modes is unclear, for the reasons described above. 

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