Nonbonded Molecular Interaction Controls Aggregation Kinetics of Hydrophobic Molecules in Water

Molecular aggregation frequently occurs during material synthesis, cellular processes, and drug delivery systems, often resulting in decreased performance and efficiency. One major reason for such aggregation in an aqueous solution is hydrophobicity. While the basic understanding of the aggregation process of hydrophobic molecules from a thermodynamic standpoint is known, the present literature lacks a connection between the aggregation kinetics and the molecular basis of hydrophobicity. This study explores how various fluorescent probes (rhodamine dyes) aggregate in an aqueous solution due to their hydrophobicity. The method employs a combination of modeling and characterization to comprehend the aggregation process by examining the nonbonded intermolecular interactions. The aggregation kinetics was analyzed by measuring the average diffusivity of the molecules using fluorescent correlation spectroscopy and NMR diffusion measurements. Through all-atom molecular dynamics (MD) simulations, it has been observed that the level of hydrophobicity is strongly correlated to the total number of hydrogen bonds between water molecules and dyes. In addition, the aggregation frequency of colliding species, which depends on the concentration, is inversely related to hydrogen bonding and the diffusivity of the molecules. This study of small molecules was applied to predict protein aggregation rates, demonstrating strong alignment with the existing literature. The study has also helped to identify and understand the concentration at which a hydrophobic molecule does not aggregate in an aqueous solution. The method developed here could help investigate the aggregation process and its root causes at the molecular level in aqueous systems to develop strategies to control it. © 2025 American Chemical Society.