Molecular recognition plays an important role in a wide range of biological and chemical applications. A particular challenge is designing selective hosts capable of recognizing subtle structural changes in guest molecules. A class of synthetic oligomers known to fold into well-defined secondary structures in solutions, termed foldamers, has been shown to form helical capsules that recognize and bind a variety of ligands in a unique flexible fashion. Selective encapsulation of monosaccharides is extremely challenging in part due to the complexity of the carbohydrate structures. For example, galactose has four isomers, α, β-D-galactopyranose and α, β-D-galactofuranose, where two of these isomers predominate. In recent experimental studies, a foldamer capsule designed from units of pyridine, quinolone, napthyridine, pyridazine, and hydrazine has been shown to be able to bind with fructose molecules with high affinity. Molecular dynamic (MD) simulations of such system reveals the atomic level mechanistic details and most importantly the dynamical information of the sugars inside the capsule. We report here a molecular dynamics study of β-D-galactopyranose and β-D-galactofuranose binding to a foldamer capsule with similar sequence and larger inside cavity. Our force field parameters, specifically adjusted for arylamide foldamers, allow us to capture important details of sugar dynamics and binding modes inside the capsule. The results will provide insight towards refining the foldamer sequence to selectively bind the different isomers of galactose. Our overall aim is to provide a general strategy in molecular recognition for the rational design of a foldamer capsule with higher specificity towards any specific sugar.

Molecular dynamics study of the selective encapsulation of galactose by arylamide foldamers

251st National Meeting (2016)

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