Molecular dynamics investigations of an indicator displacement assay mechanism in a liquid crystal sensor

A recently reported liquid-crystal sensor system based on the substrate competitive inclusion effects of β-cyclodextrin (β-CD) has been investigated using molecular dynamics simulations in this work. In such a system, the released indicator could induce an orientational transition of liquid-crystals from planar to homeotropic. The analyte molecule can thus be easily and efficiently detected by observing the corresponding optical image changing from bright to dark. Here, the different binding affinity of β-CD for the indicator (sodium dodecyl sulfate, SDS) and the analyte (methylene blue, MB) was identified using molecular dynamics simulations and absolute binding free energy calculations. The inclusion processes calculated using the adaptive biasing force algorithm can completely explain the competitive inclusion between MB and SDS by β-CD, and thus lead to a significant change in the liquid crystal optical properties.