Shape recognition

Another informative test mixture is that described by Tanaka [43], in which selectivity between triphenylene (TRI) and o-terphenyl (o-TER) is used to characterize the shape recognition capability of LC stationary phases. The primary difference between these two solutes is their planarity TRI is a planar PAH and o-TER possesses... 

Reversed-phase liquid chromatography shape-recognition processes are distinctly limited to describe the enhanced separation of geometric isomers or structurally related compounds that result primarily from the differences between molecular shapes rather than from additional interactions within the stationary-phase and/or silica support. For example, residual silanol activity of the base silica on nonend-capped polymeric Cis phases was found to enhance the separation of the polar carotenoids lutein and zeaxanthin [29]. In contrast, the separations of both the nonpolar carotenoid probes (a- and P-carotene and lycopene) and the SRM 869 column test mixture on endcapped and nonendcapped polymeric Cig phases exhibited no appreciable difference in retention. The nonpolar probes are subject to shape-selective interactions with the alkyl component of the stationary-phase (irrespective of endcapping), whereas the polar carotenoids containing hydroxyl moieties are subject to an additional level of retentive interactions via H-bonding with the surface silanols. Therefore, a direct comparison between the retention behavior of nonpolar and polar carotenoid solutes of similar shape and size that vary by the addition of polar substituents (e.g., dl-trans P-carotene vs. dll-trans P-cryptoxanthin) may not always be appropriate in the context of shape selectivity. 

Sander et al. [63] investigated the effect of microparticulate silica pore size on the properties of solution-polymerized Cig stationary phases and observed both an increase in bonding density and shape recognition for wider pore (>120 A) silica. A size-exclusion mechanism was proposed, in which the reaction of the silane polymer on the surface is enhanced for wide pores and reduced for narrow pores. Polymeric Ci8 phases prepared on substrates with narrow pores exhibited monomeric-like chromatographic properties. This effect may be the result of an increase in competitive surface linkage with the less sterically hindered monomers that coexist with the bulkier oligomers that have polymerized in the reaction solution (Figure 5.13). 

Wise, S.A. and Sander, L.C., Molecular shape recognition for polycyclic aromatic hydrocarbons in reversed-phase liquid chromatography, in Jinno, K. (Ed.), Chromatographic Separations Based on Molecular Recognition, Wiley-VCH, Inc., New York, 1997, p. 1. 

Sander, L.C. and Wise, S.A., The influence of stationary-phase chemistry on shape recognition in liquid chromatography. Anal. Chem., 67, 3284, 1995. 

The basic idea of alignment-free shape matching is that a set of rotation- and translation-free descriptors are calculated for con-formers under consideration, and then some similarity measure is devised to quantify the similarity between two molecular objects. Zauhar s shape signatures (45), Breneman s PEST and PESD methods (54-56), the USR (ultrafast shape recognition) method... 

The USR (Ultrafast Shape Recognition) Method. This method was reported by Ballester and Richards (53) for compound database search on the basis of molecular shape similarity. It was reportedly capable of screening billions of compounds for similar shapes on a single computer. The method is based on the notion that the relative position of the atoms in a molecule is completely determined by inter-atomic distances. Instead of using all inter-atomic distances, USR uses a subset of distances, reducing the computational costs. Specifically, the distances between all atoms of a molecule to each of four strategic points are calculated. Each set of distances forms a distribution, and the three moments (mean, variance, and skewness) of the four distributions are calculated. Thus, for each molecule, 12 USR descriptors are calculated. The inverse of the translated and scaled Manhattan distance between two shape descriptors is used to measure the similarity between the two molecules. A value of 1 corresponds to maximum similarity and a value of 0 corresponds to minimum similarity. 

Ballester, P. J., Finn, P. W., Richards, W. G. (2009) Ultrafast shape recognition evaluating a new ligand-based virtual screening technology. J Mol Graph Model 27, 836-845. 

Fig. 2.1 Shape recognition by the binding site increases with the geometrical complexity of the site. The number DOF represents the degrees of freedom that must be satisfied for a perfect fit...

Another way to realize the shape recognition ability is through the process known as molecular imprinting (Diaz-Garcia and Badia, 2004 Haupt, 2004). The process is depicted in Fig. 2.6. 

The extraordinary specificity of enzymatic catalysis is due to the shape recognition. Enzymes are proteins having a stereospecific binding site. At this site, the two reactants (in the above example, D-glucose and oxygen) are brought together in a precise and favorable orientation for the reaction to take place. 

Fig. 9.28 Color changes in 6 x 6 array of solvatochromic, pH-sensitive and shape-recognition dyes when exposed to ammonia (adapted from Suslick, 2004)...

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