Computational Approaches in the Design of Synthetic Receptors - Designing Receptors for the Next Generation of Biosensors - page 139

Fig. 2 Interactions between microcystin-LR and monomers. Microcystin-LR, in lines in the
center of the picture, interacts with six molecules of urocanic acid ethyl ester (UAEE) and 1
molecule of AMPSA [ 64 ]( right ) shown as ball and stick . Reproduced with permission

virtual library of monomers and molecular models of template. Examples include
Agile Molecule, Sirius, SYBYL, Oscail X, and MOE.

2.1.3 Screening of the Virtual Library

The quantity and quality of MIP recognition sites that result due to a binding event
are a direct function of the nature and extent of the monomer-template interactions
present in the pre-polymerization mixture. The previous research directed toward
understanding the physical basis of molecular recognition has shown that the extent
of template complexation at equilibrium is governed by the change in Gibbs free
energy of template-functional monomer interaction [ 125 - 127 ]. Andrews et al.
[ 128 ] detailed an approach to calculate the average binding energies of ten common
functional groups based on an analysis of structural factorization of the energetic
contributions to binding. These approaches detailed the importance of each of the
physical entities that govern a molecular recognition event. The general thermody-
namic explanation which summarizes contribution of individual physical
parameters in a binding event has been described by Williams [see Eq. ( 1 )]:

X

D G bind ¼ D G tþr þ D G r þ D G h þ D G vib þ D G p þ D G conf þ D G vdW : (1)