Origin of Co-Conformational Selectivity in a [3]rotaxane

Abstract

Co-conformational selectivity and structure-energy relationships in a [3]rotaxane are investigated with a recently developed multiple-sampling and statistical analysis procedure for modeling interlocked molecules and mechanical molecular devices. The results presented confirm the experimentally observed co-conformational selectivity. The theoretical calculations reveal that ring-ring interactions are very small and ring-shaft inter-component interactions decide the co-conformational preference. In particular, it is found that stronger ring binding at the central binding station on the shaft than at either of the two terminal binding stations gives rise to the observed co-conformational preference. Analysis of radius of gyration data shows that co-conformational isomerism is not strongly correlated to coiling of the shaft.

Working Mechanism for a Redox Switchable Molecular Machine Based on Cyclodextrin: A Free Energy Profile Approach

“…Theoretical studies of these large molecular devices, however, pose a big challenge for computational chemistry. Semiempirical quantum chemistry treatments have thus far been proved to be a judicious approximation 20,21 for some systems, where hydrogen-bonding governs the intercomponent interaction. On the other hand, molecular mechanics (MM), which readily allows energy minimization and searching through large configurational space, also provides an efficient tool for the exploration of the potential energy surface.…”

“…Theoretical studies of these large molecular devices, however, pose a big challenge for computational chemistry. Semiempirical quantum chemistry treatments have thus far been proved to be a judicious approximation , for some systems, where hydrogen-bonding governs the intercomponent interaction. On the other hand, molecular mechanics (MM), which readily allows energy minimization and searching through large configurational space, also provides an efficient tool for the exploration of the potential energy surface. – Under the circumstance where the structures of the two encircled components are analogous, the free energy difference between these coconformations can be directly compared by means of the free energy perturbation method. , Recently, the free energy profiles for the macrocycle along the switching pathway were studied by using molecular dynamics (MD) simulation. , …”

How Can Rotaxanes Be Modified by Varying Functional Groups at the Axle?—A Combined Theoretical and Experimental Analysis of Thermochemistry and Electronic Effects

“…The examination of the co-conformational selectivity of two dibenzo- [24]crown-8 macrocycles to different ammonia binding sites in a [3]rotaxane by the AM1 method or the estimation of hydrogen-bond enthalpies in polymeric urethane rotaxanes in terms of a mean-field model are examples of semiempirical approaches to supramolecular rotaxane chemistry. [10,11] A detailed study of amide-type rotaxane formation based on the AM1 level of theory including comparisons with experimental data was published by Peyerimhoff et al two years ago, in which special attention was paid to the non-covalent interactions governing the formation process. [12,13] These interactions were also studied by use of density functional theory (DFT) in small appropriate model systems ("rotaxane mimics"), and two of these model systems will also be covered in the present work.…”

“…The examination of the co‐conformational selectivity of two dibenzo‐[24]crown‐8 macrocycles to different ammonia binding sites in a [3]rotaxane by the AM1 method or the estimation of hydrogen‐bond enthalpies in polymeric urethane rotaxanes in terms of a mean‐field model are examples of semiempirical approaches to supramolecular rotaxane chemistry 10. 11 A detailed study of amide‐type rotaxane formation based on the AM1 level of theory including comparisons with experimental data was published by Peyerimhoff et al.…”

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

“…Molecular mechanics calculations were used for a free energy calculation of an α-cyclodextrin rotaxane system and for the investigation of low-barrier molecular rotary motors with rotaxane architecture [24]. The co-conformational selectivity of two dibenzo-24-crown-8 macrocycles to ammonia binding sites in a [3]rotaxane [25], and the hydrogen bonding strength in polymeric urethane rotaxanes in a mean-field model [26] were investigated by semiempirical methods.…”