Unveiling the Hidden Movements in the Shuttling of Rotaxanes

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doi: 10.1007/s40242-020-0092-4

Article

Unveiling the Hidden Movements in the Shuttling of Rotaxanes GUO Yichang1, FU Haohao1, SHAO Xueguang1,2* and CAI Wensheng1* 1. Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, P. R. China; 2. State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, P. R. China Abstract Movements in molecular machines are usually diverse and coupled, but some of them are often implicit and hard to be observed in experiments. In the present work, the two- or three-dimensional free-energy landscapes characterizing the coupled shuttling and other movements of a series of pH-triggered rotaxanes composed of a crown ether and an H-shaped axle with distinct number of phenyl rings(n=1―3) have been explored. The results show that although the calculated free-energy barriers against shuttling in the rotaxanes(n=2 and 3) change slightly, the movements coupled with the shuttling vary significantly with the axle length. At high pH, the shuttling in the rotaxane of n=2 is coupled with the isomerization of the wheel, while the shuttling in the one of n=3 is accompanied by both the isomerization and the rotation of the macrocycle. In addition, the crown ether underwent greater conformational change during shuttling at low pH compared to that at high pH. These results indicate that disentangling the coupled movements is important to reveal the underlying molecular mechanism of the shuttling. Keywords Rotaxane; Molecular machine; Molecular movement; Free-energy landscape

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Introduction

axle. In a recent study of Gholami et al.[13], the shuttling rates of a series of H-shaped rigid molecular shuttles composed of a chain with different number of phenyl rings(n=1―4) threaded onto a crown ether were investigated by NMR. In contrast with the aforementioned pillararene-based rotaxane, in this molecular object, the axle length does not influence the pH-dependent shuttling rate of the macrocycle unless the chain is short enough to let the ring simultaneously interact with the two binding sites on each end of the axle. What is the true nature of the influence of the chain length on the shuttling? In addition, it yet remains unclear whether the same shuttling rate predicts the same shuttling behavior, and whether there are other coupled movements that have not been revealed by experiments. To this end, the free-energy landscapes describing the shuttling were determined in the acid and neutral environments using the well-tempered meta-extended adaptive biasing force (WTM-eABF)[14―16] method. The effect of chain length on the shuttling of the macrocycle was explored, and the details of the shuttling processes were revealed.

Synthetic molecular machines are applied in a variety of fields, such as material science[1], drug delivery[2], catalysts[2], and the control of electrical conductivity[3]. The rational design of artificial structures with desired motions has been a challenging task for scient