Modeling of a Rotaxane-based Molecular Device
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Modeling of a Rotaxane-based Molecular Device Xiange Zheng and Karl Sohlberg Department of Chemistry, Drexel University, Philadelphia, PA 19104 ABSTRACT A computational procedure is presented for investigating photo-induced switchable rotaxanes and demonstrated for a known system. This procedure starts with the generation of more than 104 chemically reasonable rotaxane conformations based on an empirical intramolecular potential energy function. Single-point energy calculations at the semi-empirical (AM1) level are carried out for each structure in the singlet (ground), triplet, and anionic doublet states. The structural features are assigned and then correlated with energy for each state. What emerges is a profile of the structure-energy relationship that captures the salient features of the system that endow it with device-like character. Full geometry optimization of a subset of coconformations (~1%) demonstrates that the procedure based on single-point calculations is sufficient to obtain a profile of the relationship of structural features to energy that is consistent with experiments, at greatly reduced computational cost. INTRODUCTION The design, synthesis and characterization of stimuli-responsive molecular devices and machines presents a great challenge. The chemistry of macromolecular systems, especially rotaxanes, has been of considerable interest in recent years[1-5] in part because they hold promise for the fabrication of prototype molecular devices. A rotaxane is an assembly of mechanically interlocked molecules in which a dumbbell-shaped component is encycled by one (or more) chemically independent cyclic component(s). To facilitate the systematic design and refinement of functional molecular devices, it would be desirable to have available robust and validated modeling techniques. Such molecular device systems present a formidable challenge to computational chemistry owing to the large size of the molecules involved. Nevertheless, some pioneering modeling studies have been reported[5-7]. Here we demonstrate, on an experimentally realized example, a procedure for modeling rotaxane-based molecular devices that captures the features critical to their device-like character. Specifically, the modeling procedure predicts the spontaneous shuttling of the ring relative to the shaft in a switchable rotaxane, herein for a system with redox-dependant bi-stability. The overall procedure accurately captures the structural and switching characteristics of the physical system, ergo: the method shows promise to serve as a tool for molecular-device “design engineering”. COMPUTATION METHOD Initial rotaxane structure generation was performed with a graphical-user-interface molecular editor[8]. Starting structures for conformational searching were generated by stepwise translation and rotation of the crown component about the shaft component in the initial rotaxane structure. The SCAN module in the Tinker molecular mechanics (MM) software[9] was employed for the conformational searching over the full torsional s
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