Metal—macromolecule interactions

The use of molecular mechanics as an aid in the interpretation of spectroscopic data is outlined in more detail in Chapter 9. One of the most rapidly developing applications of molecular mechanics is the use of the structures to aid in the analysis of multidimensional NMR spectroscopy125,261. This is particularly pertinent to the study of metal-macromolecule interactions where the spectroscopic data often have too low an observation/variable ratio to allow an unequivocal determination of the structure. Therefore, an additional source of structural information is needed. To date, there have been a limited number of studies involving metal ions but this area is likely to become a very important application of structural information from molecular mechanics studies (see also Chapter 9). 

Two types of information are obtained from any molecular mechanics study, the minimum value of the strain energy and the structure associated with that minimum. Agreement between the energy-minimized and experimental (crystallographic) structures has often been used as the primary check on the validity of the force field and to refine the force field further, but often little predictive use has been made of the structures obtained. As force fields become more reliable, the potential value of structure predictions increases. More importantly, when no unequivocal determination of a structure is available by experimental methods then structure prediction may be the only means of obtaining a three-dimensional model of the molecule. This is often the case, for instance, in metal-macromolecule adducts, and structures obtained by molecular mechanics can be a genuine aid in the visualization of these interactions. In this chapter we consider the ways in which structure prediction by molecular mechanics calcluations has been used, and point to future directions. 

In the following chapters the complex reaction of metals with macromolecules is discussed separately for each metal ion. To conclude this series an attempt will be made to correlate metal-polynucleotide interactions with biochemical pathways. 

Dhal, P.K. Arnold, F.H. Metal-coordination interactions in the template-mediated synthesis of substrate-selective polymers recognition of bis(imidazole) substrates by copper(ii) iminodiacetate containing pol mers. Macromolecules 1992, 25, 7051-7059. 

Macromolecular complexes (MMCs) that contain at a macromolecule, a metal ion or metal complex interacting ionic by bonds (electrostatically), donor-acceptor bonds (coordinative bonds), or covalent bonds (Fig. 4). In these, the metal MMC is a specific pendant substitute. 

The results obtained demonstrate competition between the entropy favouring binding at bumps and the potential most likely to favour binding at dips of the surface. For a range of pairwise-additive, power-law interactions, it was found that the effect of the potential dominates, but in the (non-additive) limit of a surface of much higher dielectric constant than in solution the entropy effects win. Thus, the preferential binding of the polymer to the protuberances of a metallic surface was predicted [22]. Besides, this theory indirectly assumes the occupation of bumps by the weakly attracted neutral macromolecules capable of covalent interaction with surface functions. 

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