Supra-molecular chemistry is a branch of chemistry concerned with the aggregation of molecules into large assemblies. The molecules in the assembly are held by the weak intermolecular forces such as hydrogen bonding, dipolar, Vander Waal's and hydrophobic interaction and also metal ion coordination. Just as in a molecule atoms are held together by strong covalent bonds, in Supra-molecular structure, molecules are held together by weak intermolecular forces. It is often described as chemistry beyond the molecule.
Supra-molecular chemistry involves self-assembly or spontaneous association of several (2 or more) molecular components into a discrete non-covalently bound aggregate with a well defined structure. When highly complex structures are obtained from such units, the process is sometimes called self-organization.
Self assembly involves molecular recognition processes (binding events). Molecular recognition relies upon complementary of size, shape and chemical functionalities.
The partners of supra-molecular species have been named molecular receptor and substrate. The substrate usually being the smaller component whose binding is being sought. It is also sometimes called host-guest interaction. The binding of a substrate S to a receptor R yields the supra-molecule RS and involves a molecular recognition process. In order to achieve high recognition it is desirable that the receptor and substrate be in contact over a large area. This occur when the receptor is able to wrap around its guest so as to establish numerous non-covalent binding interactions and to sense its molecular size, shape and architecture.
In addition to binding sites, the receptor also carries reactive functions, it may effect chemical transformation on the bound substrate, thus behaving as a supra-molecular catalyst.
A lipophilic membrane soluble receptor may act as a carrier effecting the translocation of the bound substrates across the membrane. Thus, molecular recognition, transformation and translocation represent some of the basic functions of supra-molecular species. Supra-molecular chemistry has thus contributed in the construction of receptors, transfer agents enzyme models and extended arrays.
The concepts of the molecular recognition and complementarity are common in biological systems. complementarity between H-bonding groups on the twin strands of DNA is what makes the double helix stable. Molecular recognition is also part of the so called 'lock and Key' mechanism of enzyme action and transport of ions across membranes.
Supra-molecular chemistry first synthetic receptors were able to recognize the simplest of the substrates, the alkali metal ions. Receptors that recognize these ions already exist in nature. An example is the ionophore valinomycin which is a cyclic peptide molecule that binds specifically K+ ions and transports them across cell membranes. Valinomycin's ability to recognize and bind K+ ions selectivity is due to its geometrical complementarity, the cavity being of the rigid size to bind K+ ions. Na+ ions are smaller and are not bound by valinomycin. In addition to geometrical complementarity, valinomycin is a good receptor because of the presence of several interaction sites (Carbonyl groups) so that strong binding is possible.
It was the search of the synthetic analogues of natural ionophores that led to the discovery of cyclic ethers or crown ethers as receptors for metal ions (pederson). Crown ethers contain oxygen atoms in a cyclic structure with a central cavity with right size to fit the target ion. e.g., 18-crown-6 and 15-crown-5
In 18-crown-6 a cavity of the right size to fit K+ ions. It can, therefore, recognise and selectively bind to K+.
Subsequently, bicyclic molecules were synthesized in which nitrogen atoms unite three ether chains. These receptor molecules are three dimensional receptors with roughly spherical cavities, that bind alkali metal ions more tightly than do the single ring crown ethers. These molecules were called Cryptands and their metal complexes Cryptates. The metal ion binding ability of cryptands is selective, i.e, they exhibit molecular recognition. The selectivity is dependent on the size of the cavity.
Tricyclic receptors have also been developed which could bind large cations such as Cs+ and also NH4+ ions in their cavity.
In all these systems, the preference for a particular metal ion depends on a subtle balance between several thermodynamic factors.
a) binding energy (enthalpy)
b) gain or loss of configurational freedom (entropy) when the solvent cage of the metal ion is replaced by the ether cage.
This is characteristic of all supra-molecular complexes.
The Crown ethers and Cryptands highlighted the features that help good molecular recognition of a substrate by a receptor and helped in the construction of new receptors. They showed forinstance, how increasingly strong selective binding results from an increasing degree of pre-organization of binding groups in the receptor.
Receptor molecule with rigid cavities have the advantage that the binding sites are already in place before a substrate is bound. The binding sites donot have to organize themselves during the process of binding. In other words, they have a high degree of pre-organization and hence exhibit good molecular recognition properties such receptor molecules with relatively rigid cavities are known in nature of particular interest is the class of naturally occurring carbohydrates called Cyclodextrins, alpha-, beta-, and gamma- which contains 6, 7 and 8 glucose units respectively, linked head to tail in a ring. These molecules have a cylindrical cavity running through their centre in which small molecules can fit. The outer face of a cyclodextrin is hydrophilic with hydroxyl groups that have H-bonding ability so that the molecule is soluble in water. The inner cavity is lined mainly with C-C and C-H groups and is hydrophobic. Hence the cavity is able to receive and bind hydrophobic molecules such as benzene and phenylmethyl ether. Such receptor-substrate complexes are also called host-guest complexes or inclusion complexes. The molecular recognition in them is governed by complementarity of size and affinity (hydrophobicity) between cyclodextrin cavity and the molecule. Cyclodextrins have been investigated as enzymes mimics that enhance the selectivity of a chemical transformation carried out on the bound substrate. It was found that the H-atoms of the benzene ring of phenyl methyl ether could be substitued by chlorine specifically in the para position when the molecule was bound with a cyclodextrin. Only the para-hydrogen protruding from the bottom of the cavity was exposed to chlorine attack.
Synthetic rigid cavity receptors are also known. For example, formaldehyde and phenol derivatives can form cyclic oligomers which adopt a cup-like shape and are called calixarenes. Synthetic methods of making a wide range of calixarenes with different numbers of phenolic groups in the calix(n)arenes, where n denotes the number of phenol groups in the ring. For e.x., calix(4)arene has four phenol groups in the ring. The lining of benzene rings in the bowl shaped cavities of calixarenes allows them to acts as 'molecular baskets' for hydrophobic substrate like toluene, benzene and xylene.
The strength with which the substrate is bound depends on the complementarity of size. For e.x., toluene is firmly embedded in the bowl of a calix(4)arene but it is only loosely bound in the large cavity of calix(8)arene. It has been found that calix(7)arene will exhibit molecular recognition towards carbon cage fullerene molecules C60 and C70. The former with a soccer ball shape is bound tightly in the cavity, whereas the latter, with a rugby ball shape, is not. This provides a means of separating the two molecules which are generally formed in an intimate mixture.
Metal ions can serve as templates, that guide ligands into a particular arrangement. They, there by, act as organizing centers for synthesis of large supra-molecular assemblies from many component parts. In other words metal templation offers an effective approach to the self assembly of recognition sites.
Metal ions that form 4 coordinate square complexes are well suited to act as 90degree corners of square supra-molecular structures.
Metal ions with tetrahedral coordination geometries have been used as organizing centers for the multistep assembly of double helices (helicates). The two ligands twist around several metal ions in a double helical fashion. The two strands in these contain metal bound bipyridine units linked together. The efficiency of the self assembly process is the result of positive co-operativity, whereby the binding of one metal ion pre-organizes the ligands to facilitate the binding of the second. In other words, the assembly process gets easier as it progresses.
Similar strategies have been used to obtain molecular assemblies described as catenanes and rotaxanes. An assembly in which one ring is linked through another is called a catenane. A rotaxane is a linear molecule threaded through a cyclic molecule. Unthreading is prevented by subsequently adding bulky end caps.
One of the goals of supra-molecular chemistry is to build synthetic systems that carry out some of the functions of biochemical systems - trans membrane ion transport, enzyme -like catalysis, conducts for channeling electrons and chemical sensors with high sensitivity and selectivity.