Effect of pH on azobenzene-4,4'-dicarboxylate/α-CD complex formation. Synthesis, kinetic study and molecular modeling simulations

Abstract

The current study focuses on the molecular behavior of the azobenzene-4,4’-dicarboxylate/ α -CD pseudorotaxane and how it is affected by changes in pH. A combination of experimental measurements and molecular simulations were used, including different computational calculations, to evaluate the kinetic and thermodynamic aspects of the formation of this mechanically bound architecture. The research involved determining the formation rate constants for these complexes at different pH values and conducting a comprehensive kinetic study. Additionally, the binding affinity and complexation reaction was analyzed using free energy profiles derived from umbrella sampling in molecular dynamics simulations. To gain a better understanding of the energetic and structural aspects of the complexes, hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) calculations were employed. The intermolecular interactions that stabilize the pseudorotaxanes were characterized using quantum theory of atoms in molecules (QTAIM) and Molecular Electrostatic Potentials (MEPs)