Dynamic molecular recognition

Static molecular recognition is similar to the interaction between a lock and key. It is a 1 1 type complexation reaction between a host molecule and a guest molecule to form a host—guest complex. To achieve advanced static molecular recognition, it is necessary to make recognition sites that are specific for guest molecules. 

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Catalysts may be able to select substrates depending on physical criteria via dynamic molecular recognition through multivalent interactions [1, 2]. These molecules, which mimic enzyme functions, yet have entirely different functions, are called synzymes . In this chapter, we will review accounts of man-made catalysts that have no metal elements [3]. 

K. Ariga, T. Nakanishi, Y. Terasaka, H. Tsuji, D. Sakai, J. Kikuchi, Piezoluminescence at the Air-Water Interface through Dynamic Molecular Recognition Driven by Lateral Pressure Application , Langmuir, 21, 976 (2005)... 

Mizuno.Y., Aida,T.,Yamaguchi, K., Chirality-Memory Molecule Crystallographic and Spectroscopic Studies on Dynamic Molecular Recognition Events by Fully Substituted Chiral Porphyrins,... 

J.A. Dynamic molecular recognition in solids A synoptic approach to structure determination in t-butylcalix[4]-arene-toluene. Supramol. Chem. 1996. 7. 79-83. 28. 

Motomura, T., Inoue, K., Kobayashi, K., and Aoyama, Y. (1991) Transition-state stabilization via dynamic molecular recognition a concerted acid-base bifunctional catalysis in ester hydrolysis. Tetrahedron Lett. 32,4657-4760. 

We have already mentioned the application of supercomputers to biochemical simulations. Internal dynamics may play an Important role In such simulations. An example would be enzyme binding-site fluctuations that modulate reactivity or the dynamics of antigen-antibody association (11). In the specific case of diffusion-controlled processes, molecular recognition may occur because of long-range sterlc effects which are hard to assess without very expensive simulations (12.)-... 

These examples show that for difficult cases, and especially when a prediction is being made, a large number of simulations may be necessary. Today, the continuing increase in computer power has made such multiple simulations possible in a reasonable time frame. Several other recent studies illustrate the scope of molecular dynamics free energy for molecular recognition problems they include studies of nucleic acids [13], proteins [14-16], and methodological studies of convergence and precision [17, 18]. Several recent reviews provide additional examples [19, 20]. 

All of the experiments in pure and mixed SSME systems, as well as in the Af-stearoyltyrosine systems, have one common feature, which seems characteristic of chiral molecular recognition in enantiomeric systems and their mixtures enantiomeric discrimination as reflected by monolayer dynamic and equilibrium properties has only been detected when either the racemic or enantiomeric systems have reverted to a tightly packed, presumably quasi-crystalline surface state. Thus far it has not been possible to detect clear enantiomeric discrimination in any fluid or gaseous monolayer state. 

FIGURE 5.17. Dynamics of molecular recognition. Binding of the target molecule to the receptor. Kinetic zone diagram and characteristic equations. Adapted from Figure 1 of reference 22, with permission from the American Chemical Society. 

FIGURE 5.18. Dynamics of molecular recognition. Binding of the target molecule to the receptor. Passage (left) from zone I to zone ID (a) and from zone I to zone IA (b). From left to right, log X — oo, 1.141, 0.5, 0 (a) — oo, —0.858, 0, 0.5 (b). Adapted from Figure 2 of reference 22, with permission from the American Chemical Society. 

Chemical templates are being increasingly employed for the development of dynamic combinatorial libraries (DCL) [94-98]. These (virtual) libraries of compounds are produced from all the possible combinations of a set of basic components that can reversibly react with each other with the consequent potential to generate a large pool of compounds. Because of the dynamic equilibria established in a DCL, the stabilization of any given compound by molecular recognition will amplify its formation. Hence the addition of a template to the library usually leads to the isolation of the compound that forms the thermodynamically more stable host-guest complex (see Scheme 37). 

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