Geometrical complementarity

Epitaxial growth of PbS under well-compressed AA monolayers is explicable in terms of the geometrical complementarity between PbS and the AA head-groups. The strong intrinsic electrostatic interaction results in a very high Pb2+ concentration at the monolayer interface. The extremely low solubility of PbS in water (KSP = 8.81 x 10 29 at 25 °C) favors its rapid and random nucleation. However, the presence of the monolayer acts to drastically diminish the reaction... 

Figure 4 Self-assembly involving geometric complementarity examples of 2-D and 3-D metallocycles...

So-called transition state analogues which bind to the enzyme more tightly than natural substrates probably do so not so much because of a geometrical complementarity to the enzyme but more as a result of compatible electrostatic interactions. For example, it seems more likely that lactones (XIX) bind to lysozyme better... 

The substrate can bind to the enzyme at the active site via noncovalent interactions (van der Waals, electrostatic, hydrogen bonding, hydrophobic), and with a specific geometric complementarity, as the surface of the active site of that enzyme is complementary in shape to the substrate. Electronic complementarities are due to the fact that the amino acid residues at the active site are arranged to interact specifically with the substrate. Although most enzymes are amino acids with hundreds of acids in the chain, the active site is the size of the substrate. Complementarity in the structure and charge between the enzyme and the substrate is illustrated by the so-called lock-and-key concept (Figure 2.15). 

B. Geometric Complementarity and Atomic Packing 1. Evaluating the Geometric Complementarity of Two Macromolecular Surfaces... 

The geometric complementarity of the two surfaces in contact, which optimizes van der Waals contacts, is a major element of the recognition process between two molecules. For proteins, geometric complementarity has been estimated in a number of different ways. 

Any classification scheme is necessarily arbitrary, but ionophores are often divided into two groups naturally occurring and synthetic. A subclassification distinguishes on the basis of open-chained (noncyclic) versus cyclic. Examples of the latter typically exceed the former because binding site preorganization and geometric complementarity are usually easier to achieve or ensure in a cyclic structure when the goal is to complex a spherical ion. 

Classical coordination compounds are formed by interactions between acceptor species (Lewis acids) and donor species (Lewis bases). When potential acceptor and donor sites are present simultaneously in the same molecule these can be described as self-complementary and their reciprocal recognition can lead to self-assembly (or self-organization). This often occurs with organometallic compounds. For self-assembly to occur an additional steric fitness or geometric complementarity is required, as shown schematically in Figure 1.1. 

In this process, every solution where there is overlapping of core locations fi om both molecules is immediately discarded and, for the remaining ones, the extent of geometric complementarity is evaluated by summing the number of overlaps between grid positions corresponding to the surface shells (Figure 2). 

Although the structure of protein-protein complexes is not fully explained by geometric complementarity, this does appear to be a fairly common and relevant feature of macromolecular associations. The results presented support the assumption that surface shape complementarity, as evaluated by surface contact, can be a useful filtering criterion to reduce the number of possible alternative geometries to a manageable size, which may then be further evaluated. 

---