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Laser-induced cross-linking of polyynes is successfully hindered when the polyyne is encapsulated as part of a rotaxane and therefore protected by a surrounding macrocycle. When the rotaxane is electrosprayed, however, noncovalent aggregate ions are efficiently formed. Aggregates of considerable size (including more than 50 rotaxane molecules with masses beyond 100k Da) and charge states (up to 13 charges and beyond) have been observed. Either protons or sodium cations act as the charge carriers. These aggregates are not formed when the individual components of the rotaxane, i.e., the macrocycle or the polyyne, are separately electrosprayed. This underlines the structural importance of the rotaxane for the aggregate formation. Straightforward force field calculations indicate that the polyyne thread hinders the folding of the macrocycles, which facilitates the bonding interaction between the two components.

We describe the thermodynamics of a solution of rotaxanes which can change their length from a short state of length L to a long state of length qL in response to their surrounding environment. We call these rotaxanes "adaptive." We show that such a system can exhibit both isotropic and nematic liquid crystalline phases. The system shows several interesting kinds of behaviour. First we predict that the fraction of short-length rotaxanes increases linearly with concentration and is a maximum at the critical concentration that marks the isotropic to nematic transition. Second, the critical concentration shows a minimum at a certain value of q. Our model suggests that the effect of adaptive length changes is most dramatic at small q and where the long state is slightly favoured.

We examine a simple model of rotaxane structure, with 3 asymmetric rings interacting via repulsive power-law forces. This interlocked molecule exhibits conformational isomerisation which is different from that of molecules whose connectedness is through covalent bonds. The rings are free to translate along and rotate around the axle, and hence weak interaction forces between the rings can lead to distinct rotamer states. We use energy minimisation to determine these states exactly, and show that there can be transitions from asymmetric to symmetric states by varying the bond lengths. We also use classical statistical mechanics to show the effect of thermal noise.

Physical systems often respond on a timescale which is longer than that of the measurement. This is particularly true in soft matter where direct experimental measurement, for example in force spectroscopy, drives the soft system out of equilibrium and provides a non-equilibrium measure. Here we demonstrate experimentally for the first time that equilibrium physical quantities (such as the mean square displacement) can be obtained from non-equilibrium measurements via umbrella sampling. Our model experimental system is a bead fluctuating in a time-varying optical trap. We also show this for simulated force spectroscopy on a complex soft molecule--a piston-rotaxane.

Computational software workflows are emerging as all-in-one solutions to speed up the discovery of new materials. Many computational approaches require the generation of realistic structural models for property prediction and candidate screening. However, molecular and supramolecular materials represent classes of materials with many potential applications for which there is no go-to database of existing structures or general protocol for generating structures. Here, we report a new version of the supramolecular toolkit, stk, an open-source, extendable, and modular Python framework for general structure generation of (supra)molecular structures. Our construction approach works on arbitrary building blocks and topologies and minimizes the input required from the user, making stk user-friendly and applicable to many material classes. This version of stk includes metal-containing structures and rotaxanes as well as general implementation and interface improvements. Additionally, this version includes built-in tools for exploring chemical space with an evolutionary algorithm and tools for database generation and visualization. The latest version of stk is freely available at github.com/lukasturcani/stk.

We examine a solution of non-adaptive two-state rotaxane molecules which can switch from a short state of length L to a long state of length qL, using statistical thermodynamics. This molecular switching is externally driven and can result in an isotropic-nematic phase transition without altering temperature and concentration. Here we concentrate on the limitation imposed by switching inefficiency, i.e., on the case where molecular switching is not quantitative, leading to a solution of rotaxanes in different states. We present switching diagrams that can guide in the design of rotaxanes which affect a macroscopic phase change.