On-the-Fly Training of Atomistic Potentials for Flexible and Mechanically Interlocked Molecules

Substitution and Orientation Effects on the Crystallinity and PFAS Adsorption of Olefin-Linked 2D COFs

Solid phase adsorbents with high removal affinity for per- and polyfluoroalkyl substances (PFAS) in aqueous environments are sought. We report the synthesis and investigation of COF-I, a new covalent organic framework (COF) with a good affinity for PFAS adsorption. COF-I was synthesized by the condensation reaction between 2,4,6-trimethyl-1,3,5-triazine and 2,3-dimethoxyterephthaldehyde and fully characterized. In addition to the high crystallinity and surface area, COF-I showed high hydrolytic and thermal stability. Further, we converted its hydrophobic surface to a hydrophilic surface by converting the ortho-methoxy groups to hydroxyl derivatives and produced a new hydrophilic olefin-linked two-dimensional (2D) COF. We experimentally measured the crystallinity of both COFs by X-ray diffraction and used atomistic simulations coupled with cross-polarization/magic angle spinning solid-state nuclear magnetic resonance (CP/MAS ssNMR) to determine the relative amounts of AA-stacking and AB-stacking present. COF-I, with its hydrophobic surface and methoxy groups in the ortho positions, showed the best PFAS adsorption. COF-I reduced the concentration of perfluorooctanoic acid from 20 to 0.069 μg L-1 and to 0.052 μg L-1 for perfluorooctanesulfonic acid. These amounts are lower than the U.S. Environmental Protection Agency advisory level (0.070 μg L-1). High efficiency, fast kinetic adsorption, and reusability of COF-I are advantages of COF-I for PFAS removal from water.

Theoretical trends in the dynamics simulations of molecular machines across multiple scales

Over the past few decades, molecular machines have been extensively studied, since they are composed of single molecules for functional materials capable of responding to external stimuli, enabling motion at scales ranging from the microscopic to the macroscopic level within molecular aggregates. This advancement holds the potential to efficiently transform external resources into mechanical movement, achieved through precise control of conformational changes in stimuli-responsive materials. However, the underlying mechanism that links microscopic and macroscopic motions remains unclear, demanding computational development associated with simulating the construction of molecular machines from single molecules. This bottleneck has impeded the design of more efficient functional materials. Advancements in theoretical simulations have successfully been developed in various computational models to unveil the operational mechanisms of stimulus-responsive molecular machines, which could help us reduce the costs in experimental trial-and-error procedures. It opens doors to the computer-aided design of innovative functional materials. In this perspective, we have reviewed theoretical approaches employed in simulating dynamic processes involving conformational changes in molecular machines, spanning different scales and environmental conditions. In addition, we have highlighted current challenges and anticipated future trends in the collective control of aggregates within molecular machines. Our goal is to provide a comprehensive overview of recent theoretical advancements in the field of molecular machines, offering valuable insights for the design of novel smart materials.

Into the dynamics of rotaxanes at atomistic resolution

Mechanically-interlocked molecules (MIMs) are at the basis of artificial molecular machines and are attracting increasing interest for various applications, from catalysis to drug delivery and nanoelectronics. MIMs are composed of mechanically-interconnected molecular sub-parts that can move with respect to each other, imparting these systems innately dynamical behaviors and interesting stimuli-responsive properties. The rational design of MIMs with desired functionalities requires studying their dynamics at sub-molecular resolution and on relevant timescales, which is challenging experimentally and computationally. Here, we combine molecular dynamics and metadynamics simulations to reconstruct the thermodynamics and kinetics of different types of MIMs at atomistic resolution under different conditions. As representative case studies, we use rotaxanes and molecular shuttles substantially differing in structure, architecture, and dynamical behavior. Our computational approach provides results in agreement with the available experimental evidence and a direct demonstration of the critical effect of the solvent on the dynamics of the MIMs. At the same time, our simulations unveil key factors controlling the dynamics of these systems, providing submolecular-level insights into the mechanisms and kinetics of shuttling. Reconstruction of the free-energy profiles from the simulations reveals details of the conformations of macrocycles on the binding site that are difficult to access via routine experiments and precious for understanding the MIMs' behavior, while their decomposition in enthalpic and entropic contributions unveils the mechanisms and key transitions ruling the intermolecular movements between metastable states within them. The computational framework presented herein is flexible and can be used, in principle, to study a variety of mechanically-interlocked systems.

Dynamic network of intermolecular interactions in metal-organic frameworks functionalized by molecular machines

Molecular machines enable external control of structural and dynamic phenomena at the atomic level. To efficiently transfer their tunable properties into designated functionalities, a detailed understanding of the impact of molecular embedding is needed. In particular, a comprehensive insight is fundamental to design hierarchical multifunctional systems that are inspired by biological cells. Here, we applied an on-the-fly trained force field to perform atomistic simulations of a systematically modified rotaxane functionalized metal-organic framework. Our atomistic studies reveal a symmetric and asymmetric interplay of the mechanically bonded rings (MBRs) within the framework depending on the local environment. As a result, their translational motion is modulated ranging from fast oscillatory behavior to cooperative and potentially directed shuttling. The derived picture of competitive interactions, which influence the operation mechanism of the MBRs embedded in these soft porous materials, promotes the development of responsive functional materials, which is a key step toward intelligent matter.