The interlocking process in molecular machines explained by a combined approach: the nudged elastic band method and a machine learning potential

Abstract

Engineering molecular machines requires a precise knowledge of the mechanisms involved in programmed motions. Among artificial molecular machines, rotaxanes have emerged as a noteworthy model due to their ability to perform diverse and controlled motions, such as threading, shuttling, and pirouetting. In this work, we present a reliable theoretical framework to describe the threading motion during the assembly of rotaxane-like complexes. Our approach combines the climbing image Nudged Elastic Band method with the ANI-1ccx neural network potential, trained with gold-standard data. Energetic and structural variations along a normalized displacement coordinate allowed an accurate atomistic description of the threading process of different dumbbell-shaped molecules (axles) through the cavity of two different macrocyclic hosts (tori). Using the methodology herein proposed, two key steps are identified: stabilization through hydrogen bonds, which we call the claw mechanism, and the expansion of the macrocycle. An energy decomposition analysis, performed by single-point calculations on selected structures, allows analyzing the role of steric and electrostatic effects in the structural stabilization of the supramolecular assemblies. We find that, although ANI-1ccx was not explicitly trained for charged systems, this neural network potential effectively discriminates between different charged states. Furthermore, calculated potential energy barriers are in good agreement with experimental free energy barriers reported. The featured methodology has the potential to become a fundamental artificial intelligence-based tool for the study of diverse motions observed in supramolecular systems.