Abstract
<jats:p>Constitutional isomerism is among the most fundamental forms of molecular structural variation, yet how it governs molecular recognition across multiple physicochemical scales remains largely unexplored. Here we establish a multiscale computational framework to uncover how constitutional isomerism reprograms host-guest recognition in carbohydrate macrocycles by comparing cyclodextrins and their constitutional isomers, cyclodextrans. Using force-field reparameterization, equilibrium enhanced sampling, nonequilibrium alchemical simulations and quantum-mechanical energy decomposition analysis, we systematically investigate cyclodextrins and cyclodextrans of varying sizes and 130 host-guest complexes involving these carbohydrate macrocycles. We show that replacing α-(1→4) with α-(1→6) glycosidic linkages fundamentally reshapes conformational landscapes, transforming rigid preorganized cavities into highly adaptive recognition architectures with multiple competing binding pathways. Despite this pronounced structural heterogeneity, thermodynamic predictability is preserved when conformational ensembles are rigorously resolved. More importantly, constitutional isomerism rewires interaction fingerprints and establishes distinct physicochemical recognition classes despite identical monosaccharide composition. These findings reveal a topology-driven mechanism that propagates from molecular connectivity to conformational dynamics, recognition mechanisms and interaction physics, providing general design principles for programmable molecular recognition in flexible supramolecular systems.</jats:p>