2.1 Definition of Molecular Recognition

Molecular recognition is the binding and specific selection of substrate(s) by a given receptor molecule. It is found in both organic and inorganic realms, from the lowest level to the highest. Examples (in increasingly larger systems) could be the recognition of the ammonium ion (diameter 3.4 angstroms) by a macrotricyclic cryptand, catalysis, the first step in an enzymatic reaction involving lysozyme (an ellipsoid measuring roughly 45 by 30 by 30 angstroms), and the self-replication of DNA (microns in length). Mere binding is not recognition, although it is often taken as such. Molecular recognition implies a pattern-recognition process through a structurally well-defined set of intermolecular interactions defining the processing algorithm. Binding of a receptor ρ (bigger part) to a substrate σ (smaller part) forms a complex, or supermolecule, characterized by its thermodynamic and kinetic stability and selectivity (i.e., by the amount of energy and of information brought into the operation).

The major difference between supramolecular chemistry^[1] and molecular chemistry is in the type of bonds used. Whereas molecular chemistry is based on the covalent bond, supramolecular chemistry implements the intermolecular noncovalent types of binding (electrostatic interactions, hydrogen bonding, van der Waals forces, etc.). The latter are usually weaker than covalent bonding, hence supramolecular species are thermodynamically less stable, kinetically more labile, and dynamically more flexible than molecules. This "soft bonding", allowing for a more flexible exploration of the available energy surface, will turn out to have many interesting ramifications.

The effects resulting from molecular recognition are wide ranging. The physical characteristics of the supermolecule can differ radically from that of either the substrate or receptor alone, with corresponding effects on reactivity, optical behavior, charge distribution, and so forth. "Information" in a supermolecule may be stored in multiple forms: in the architecture of the receptor, in its binding sites, and in the ligand layer surrounding the bound receptor. Depending on the characteristics of the supermolecule, this information may be observed directly (as in the case of fluorescence or a chemical reaction occurring) or may contribute to such secondary effects as reactivity, kinetic effects and so on. In many cases, the receptor may strain the substrate, allowing easier cleavage (photoinduced or through the action of a third molecule). For receptors with two or more recognition sites, molecular recognition may bring components into close proximity, facilitating chemical reactions, energy transfer, or charge transfer, just to name a few possibilities.

Molecular recognition has a critical role to play in such areas as catalytic activity and membrane transport as well. Finally, there is the possibility of inducing nonlinear effects such as self-assembly and self-organization, which can lead to massive signal amplification and macroscopic changes of state. In fact, much of supramolecular chemistry can be said to concern either molecular recognition or its application, and most, if not all, biological processes involve a molecular recognition event at some stage. This chapter can only give a brief overview of this fascinating field.

^[1]The difference between supermolecular chemistry and supramolecular chemistry is that although the former is limited to the specific chemistry of the supermolecules themselves, supramolecular chemistry is broader, concerning the chemistry of all types of supramolecular entities from the well-defined supermolecular to extended, more or less organized, polymolecular associations.