Synthetic light-driven rotary molecular motors show complicated structural dynamics during the rotation process. A combination of DFT calculations and various spectroscopic techniques is employed to study the effect of the bridging group in the lower half of the molecule on the conformational dynamics. It was found that the extent to which the bridging group can accommodate the increased folding in the transition state is the main factor in rationalizing the differences in barrier height and, as a consequence, the rotary speed. These findings will be essential in designing future rotary molecular motors.

We present a novel method for investigating the self-assembly process by following the average composition of the fragmentary species.

The self-assembly process of a Pd L cage complex consisting of rigid ditopic ligands, in which two 3-pyridyl groups are connected to a benzene ring through acetylene bonds and Pd ions was revealed by a recently developed quantitative analysis of self-assembly process (QASAP), with which the self-assembly process of coordination assemblies can be investigated by monitoring the evolution with time of the average composition of all the intermediates. QASAP revealed that the rate-determining steps of the cage formation are the intramolecular ligand exchanges in the final stage of the self-assembly: [Pd L Py* ] →[Pd L Py* ] +Py* and [Pd L Py* ] →[Pd L ] +Py* (Py*: 3-chloropyridine, which was used as a leaving ligand on the metal source). The energy barriers for the two reactions were determined to be 22.3 and 21.9 kcal mol , respectively. DFT calculations of the transition-state (TS) structures for the two steps indicated that the distortion of the trigonal-bipyramidal Pd center at the TS geometries increases the activation free energy of the two steps.

The effect of reaction environment on the self-assembly process of an octahedron-shaped PdL capsule was investigated. Quantitative analysis of self-assembly process with H NMR spectroscopy revealed that the self-assembly pathway of the capsule was altered by solvent and a leaving ligand coordinating to the metal source, which are not the components of the final self-assembly. Solvents definitively determine the pathway ofthe self-assembly at a very early stage of the self-assembly. Contrary to the expectation that the weaker the coordination ability of the leaving ligand is, the faster the formation of the final assembly becomes, a leaving ligand with weak coordination ability tends to generate a kinetically trapped species to prevent the capsule formation under mild conditions.

Kinetic control of molecular self-assembly remains difficult because of insufficient understanding of molecular selfassembly mechanism. Here we report the formation of a metastable [Pd2L4] 4+ cage structure composed of naphthalene-based ditopic ligands (L) and Pd(II) ions in very high yield (99%) under kinetic control by modulating the energy landscape. The guest anion trapped in the cage and the solvent with very weak coordination ability prefer the formation of suitable intermediates and prevent the conversion of the metastable cage into the thermodynamically most stable decomposed state. The cage formation pathways under kinetic control and the effect of the anions encapsulated on the self-assembly processes were investigated by QASAP (quantitative analysis of self-assembly process) and NASAP (numerical analysis of self-assembly process). It was found that the self-assembly with a preferred guest (BF4-) proceeds through intermediates composed of no more components than the cage ([PdaLbXc] 2a+ (a ≤ 2, b ≤ 4, X indicates a leaving ligand)) and that the final intramolecular cage-closure step is the rate-determining step. In contrast, a weaker guest (OTf-) causes the transient formation of intermediates composed of more components than the cage ([PdaLbXc] 2a+ (a > 2, b > 4)), which are finally converted into the cage.