Supramolecular Catalysis of m-Xylene Isomerization by Cucurbiturils: Transition State Stabilization, Vibrational Coupling, and Dynamic Binding Equilibrium

Kinetics from Metadynamics: Principles, Applications, and Outlook

Metadynamics is a popular enhanced sampling algorithm for computing the free energy landscape of rare events by using molecular dynamics simulation. Ten years ago, Tiwary and Parrinello introduced the infrequent metadynamics approach for calculating the kinetics of transitions across free energy barriers. Since then, metadynamics-based methods for obtaining rate constants have attracted significant attention in computational molecular science. Such methods have been applied to study a wide range of problems, including protein-ligand binding, protein folding, conformational transitions, chemical reactions, catalysis, and nucleation. Here, we review the principles of elucidating kinetics from metadynamics-like approaches, subsequent methodological developments in this area, and successful applications on chemical, biological, and material systems. We also highlight the challenges of reconstructing accurate kinetics from enhanced sampling simulations and the scope of future developments.

Modulating the reaction pathway of phenyl diazonium ions using host-guest complexation with cucurbit[7]uril

Aryl diazonium ions are known to be an important intermediate in the divergent synthesis of azo compounds and substituted aromatics. The presence of more than one electrophilic center in a diazonium ion could lead to undesirable side reactions during a synthesis. Herein, we report that the electrophilic α-carbon on a phenyl diazonium [PhN₂]⁺ ion can be selectively deactivated upon host-guest complexation with cucurbit[7]uril (CB7) in aqueous media, achieving a ∼60-fold increase in the half-life of [PhN₂]⁺. Notably, however, the electrophilic nitrogen of the encapsulated diazonium ion remains active towards diazo coupling with strong nucleophiles, allowing the formation of azo compounds using a two-month-old aqueous solution of [CB7-PhN₂]⁺. Our supramolecular approach can open new possibilities for the reactive chemistry of organic molecules in aqueous media.

Rapid Estimation of Binding Constants for Cucurbit[8]uril Ternary Complexes Using Electrochemistry

Supramolecular complexes are of fundamental interests in biomedicines and adaptive materials, and thus facile methods to determine their binding affinity show usefulness in the design of novel drugs and materials. Herein, we report a novel approach to estimate the binding constants K_G2 of cucurbit[8]uril-methyl viologen-based ternary complexes (CB8-MV²⁺-G2) using electrochemistry, achieving high precision (±0.03) and practical accuracy (±0.32) in logK_G2 and short measurement time (<10 min). In particular, we have uncovered a linear correlation (R² > 0.8) between the reduction potential of CB8-MV²⁺-G2 ternary complexes and their reported binding constants from isothermal titration calorimetry, which allow a calibration curve to be plotted based on 25 sample complexes. Mechanistic investigation using experimental and computational approaches reveals that this correlation stems from the dynamic host-guest exchange events occurring after the electron transfer step. Binding constants of unknown ternary complexes, where G2 = hydrocarbons, were estimated, illustrating potential applications for sparsely soluble second guests.