Molecular recognition shape

Biology and organic chemistry are replete with examples of self-assembly. Examples include lipid bilayers, the DNA duplex, proteins in their correctly folded forms, self-assembled monolayers, and crystals. In MESA, we extend ideas abstracted from molecular recognition - shape recognition, chirality, directional interactions, hierarchy of bonds, and hydrophobicity - to the mesoscale. 

Substrates involved in molecular recognition may feature a particular shape, size, state of charge, chemical affinity or optical specification (19,30,33—36). In general most of these parameters share. Nevertheless there may be dominating features of a certain substrate molecule to be used by a complementary receptor in the recognition process (9). 

Another synthetic strategy is based on self-assembly driven by molecular recognition between complementary TT-donors and 7T-acceptors. Examples include the synthesis of catenanes and rotaxanes that can act as controUable molecular shuttles (6,236). The TT-donors in the shuttles are located in the dumb-beU shaped component of the rotaxane and the 7T-acceptors in the macrocycHc component, or vice versa. The shuttles may be switched by chemical, electrochemical, or photochemical means. 

The Role of Molecular Shape Similarity in Specific Molecular Recognition... 

The present review intends to be illustrative rather than comprehensive, and focuses on the results of this study leading to the hypothesis 9 — the three-dimensional shape similarity between interacting groups in reacting molecules is responsible for more specific and precise molecular recognition than would otherwise be achieved — and on the explanation of biological recognition on this basis. 

The problem of molecular recognition has attracted biologically oriented chemists since Emil Fischer s lock-and-key theory l0). Within the last two decades, many model compounds have been developed micelle-forming detergents11, modified cyclodextrins 12), many kinds of crown-type compounds13) including podands, coronands, cryptands, and spherands. Very extensive studies using these compounds have, however, not been made from a point of view of whether or not shape similarity affects the discrimination. 

Another example of the shape similarity effect on molecular recognition involves the similarity between the structures of the binding sites. Investigation was made for four reaction systems I-IV each consisting of a 1 1 mixture of thiols HS—X and HS—Y... 

Crystalline 1 1 complex formation can be regarded as molecular recognition in the process of crystallization. Since the formation of a new type of the crystalline 1 1 complex depends on the shapes of R7 and R8 35), the influence of the spatial relationship between R7 and R8 on the complex formation was investigated. 

The similarity recognition hypothesis presented here would be applicable to the specific and precise discrimination in chemical and biological systems. It is hoped that this review will serve to stimulate further work on the physicochemical origin of the shape-similarity effect on specific molecular recognition, for example, work on weak interactions specific for the three-dimensional shape of interacting groups. 

To prepare artificial enzymatic systems possessing molecular recognition ability for particular molecules, molecular imprinting methods that create template-shaped cavities with the memory of the template molecules in polymer matrices, have been developed [22, 30-35] and established in receptor, chromatographical separations, fine-chemical sensing, etc. in the past decade. The molecular... 

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