The Effect of Mechanical Interlocking on Crystal Packing:  Predictions and Testing

Abstract

The first statistical analyses of the X-ray crystal structures of mechanically interlocked molecular architectures, the first molecular mechanics-based solid-state calculations on such structures and atomic force microscopy (AFM) experiments are used in combination to predict and test which types of benzylic amide macrocycle-containing rotaxanes possess mobile components in the crystalline phase and thus could form the basis of solid-state devices that function through mechanical motion at the molecular level. The statistical studies and calculations show that crystals formed by rotaxanes possess similarities and unanticipated differences with respect to the crystal packing of noninterlocked molecules. Trends in the rotaxane series correlate quantities related to crystal packing, molecular size, stoichiometry, and H-bonding. In accordance with the findings of Gavezzotti et al. for conventional molecular architectures, a principal component analysis (PCA) showed that three vectors related to the size, packing parameters, and stoichiometry are sufficient to describe the crystal properties of benzylic amide macrocycle-containing rotaxanes. When hydrogen bond-related quantities are included in a second PCA, they combine with the size and the stoichiometry vectors but not with packing-related parameters, indicating that the intramolecular "saturation" of the H-bonds (between the interlocked components) takes precedence over crystal assembly (i.e., intermolecular packing) in these systems. However, cluster analyses also suggest a major role for the energy of interaction between the macrocycle and its crystal environment. The identification of such a "privileged" interaction is of fundamental importance to the development of rotaxanes with in-crystal mobility of one or more of their interlocked components, a prerequisite for the exploitation of molecular level mechanical motion in the solid state. The set of trends found, together with the calculated energies, was used to propose guidelines for which benzylic amide macrocycle-containing rotaxanes are best suited to become building blocks for systems with mobile submolecular units in the crystalline phase. An experimental test of the predictive power of such guidelines was carried out using AFM on a rotaxane and its thread, identified by the study as a promising candidate for solid-state mobility. Intuitively, the rotaxane should be less mobile in the solid state since it has multiple sets of both hydrogen bond donors and acceptors that can form strong inter- and intramolecular H-bonds. Conversely, the thread has no hydrogen bond donors and cannot form such bonds. The AFM experiments, however, confirm the statistical analysis prediction that the rotaxane is considerably more mobile in the solid than the thread.

Infrared Study of Intercomponent Interactions in a Switchable Hydrogen‐Bonded Rotaxane

“…Molecular modeling and crystal structures of related rotaxanes [35][36][37] show that this binding motif can exist, but it probably plays a minor role. In the chlorinated solvents, this band was not found, probably because it is obscured by the strong n(CO) macro and n(CO) succ bands.…”

Rare and Diverse Binding Modes Introduced through Mechanical Bonding

“…Such a binding motif, which requires essentially orthogonal pyridine rings with the nitrogen atoms bridged by bifurcated hydrogen bonds, is extremely rare (a search of the Cambridge Crystallographic Database reveals only one other example [5] ) but is somewhat reminiscent of the hydrogen bonding that occurs at 908 to the plane of the lone pairs of amide groups in threads seen extensively in other hydrogen-bonded rotaxanes. [6] Slow cooling of a hot, saturated solution of H 2 1 in acetonitrile/chloroform (10:1) yielded single crystals that were of sufficient quality to confirm the interaction in the solid state by X-ray crystallography (Figure 3 a, b) but were inadequate to confidently characterize the interaction in detail. [7] However, when we prepared a [2]catenane that incorporated the same functional groups, H 2 2, a similar noncovalent interaction was observed in solution in CDCl 3 and, in this case, single crystals of excellent quality were obtained by slow cooling of a hot, saturated solution of H 2 2 in acetonitrile.…”

Photoisomerization of a rotaxane hydrogen bonding template: Light-induced acceleration of a large amplitude rotational motion

“…Using a computational procedure that uses the MM3 forcefield (18) and the TINKER program (19) and has proved successful in describing the circumrotation pathway in catenanes (20), macrocycle pirouetting in rotaxanes (13), and other properties in mechanically interlocked molecules (21,22), it was possible to locate the saddle points for macrocycle circumrotation in E-4 and Z-4. Fig.…”