Self-Assembly Processes of Octahedron-Shaped Pd6L4 Cages.

The self-assembly processes of two kinds of octahedron-shaped M6L4 cages consisting of cis-protected Pd(II) complexes and organic tritopic ligands were investigated. Whether kinetically trapped species larger than the cages are produced or the M6L4 cage is assembled without the formation of such kinetic traps is determined by a balance between the rates of oligomerization and intramolecular cyclization, which is affected by slight changes in the chemical structure of the tritopic ligand. A numerical analysis of the experimental data based on a reaction network model where 249 reactions between the possible 56 species were considered revealed the self-assembly pathways of one of the two M6L4 cages.

Navigated Self-Assembly of a Pd2L4 Cage by Modulation of an Energy Landscape under Kinetic Control.

Kinetic control of molecular self-assembly remains difficult because of insufficient understanding of molecular self-assembly mechanisms. 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. When self-assembly occurs with anionic guests in weakly cooordinating solvent then suitable intermedites and the metastable cage is formed. These conditions also prevent further transformation into the thermodynamically 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.

Quantitative Analysis of the Self-Assembly Process of Hexagonal PtII Macrocyclic Complexes: Effect of the Solvent and the Components.

The self-assembly process of three PtII -linked hexagonal macrocycles consisting of dinuclear PtII complexes and organic ditopic ligands was investigated in polar and less polar solvents by a recently developed approach: quantitative analysis of the self-assembly process (QASAP). In polar CD3 NO2 , for all the three macrocycles, an ML2 complex was the dominant intermediate during self-assembly, as a result of high positive allosteric cooperativity for the ligand exchange on the PtII centers of the dinuclear PtII complexes. On the other hand, in less polar CD2 Cl2 , the self-assembly process was affected by the components. For two of the three macrocycles, the chainlike oligomers that contain fewer metals and ligands than the corresponding macrocycles grew with time and the type of the chainlike intermediates formed correlated with the allostericity of the two binding sites in the organic ditopic ligands. In every case, no long oligomers containing more components than the macrocycles themselves were produced during the self-assembly even though free rotation around single bonds in the chainlike oligomers allows them to adopt various conformations that do not facilitate the cyclization. This result suggests that electrostatic and/or steric factors besides rigidity of the components make the cyclization advantageous not only thermodynamically but also kinetically.

A Balance between van der Waals and Cation-π Interactions Stabilizes Hydrophobic Assemblies.

A thermally highly stable molecular self-assembly (nanocube) in water, the decomposition temperature of which is 415 K, was developed by designing a gear-shaped amphiphile (GSA) with an indented hydrophobic surface, even though the nanocube is stabilized only by van der Waals (vdW) and cation-π interactions as well as the hydrophobic effect. The introduction of an electron-donating substituent in one of the benzene rings of the GSA increased the decomposition temperature by 12 K, which is due to the stronger cation-π interactions between the benzene ring and positively charged pyridinium rings and tighter molecular meshing between the GSAs in the nanocube. The position of the substituent introduced in the benzene ring greatly affects the thermal stability of the nanocubes, and this indicates that both vdW (molecular meshing) and cation-π interactions are crucial for improving the thermal stability of the hydrophobic assemblies.

Energy-Landscape-Independent Kinetic Trap of an Incomplete Cage in the Self-Assembly of a Pd2 L4 Cage.

A kinetic trap is the metastable species that is transiently or constantly produced during the reaction by trapping in a deep energy well. In most cases, the reactivity of kinetically trapped species is relatively low under the reaction conditions. Herein, we report another type of kinetically trapped species that is an incomplete cage (IC) intermediate produced during the self-assembly of a Pd2 L4 cage from ditopic ligand (L) and PdII ions with a certain lifetime, although IC has a high enough reactivity to be converted into the cage with the reaction of free L, which was confirmed by the reaction of the isolated IC and L under the self-assembly conditions. IC was kinetically trapped not because IC lies on the bottom of a deep energy well but because the conversion of the intermediates essential for the conversion of IC to the cage preferentially takes place; IC was kinetically trapped independently of the shape of the energy landscape of the self-assembly.

Self-Assembly Process of a Pd2 L4 Capsule: Steric Interactions between Neighboring Components Favor the Formation of Large Intermediates.

The effect of molecular interactions between the components on the self-assembly process of Pd2 L4 structures was investigated by a 1 H NMR-based quantitative approach (QASAP: quantitative analysis of self-assembly process). Although the self-assembly of the Pd2 L4 cage without interactions between the bent ligands took place, mainly producing small intermediates, the self-assembly of the Pd2 L4 capsule composed of bent ligands with anthracene panels tends to produce large intermediates containing more components than the capsule. This is ascribed to steric interactions between the panels.

Quantitative Analysis of Self-Assembly Process of a Pd2 L4 Cage Consisting of Rigid Ditopic Ligands.

The self-assembly process of a Pd2 L4 cage complex consisting of rigid ditopic ligands, in which two 3-pyridyl groups are connected to a benzene ring through acetylene bonds and PdII 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: [Pd2 L4 Py*2 ]4+ →[Pd2 L4 Py*1 ]4+ +Py* and [Pd2 L4 Py*1 ]4+ →[Pd2 L4 ]4+ +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-1 , respectively. DFT calculations of the transition-state (TS) structures for the two steps indicated that the distortion of the trigonal-bipyramidal PdII center at the TS geometries increases the activation free energy of the two steps.

Importance of Molecular Meshing for the Stabilization of Solvophobic Assemblies.

The effect of the methyl groups in neutral gear-shaped amphiphiles (GSAs) on the stability of nanocubes was investigated using a novel C2 v-symmetric GSA, which was synthesized using selective alternate trilithiation of a pentabrominated hexaphenylbenzene derivative. The lack of only one methyl group in the GSA decreased the association constant for the assembly of the nanocube by 3 orders of magnitude. A surface analysis recently developed by the authors (SAVPR: surface analysis with varying probe radii) was carried out for characteristic isomers of the nanocube consisting of C2 v-symmetric GSAs. It was found that the methyl groups near the equator of the nanocube play a significant role in the stabilization of the nanocubes.

Multiple Pathways in the Self-Assembly Process of a Pd4L8 Coordination Tetrahedron.

The self-assembly of a Pd418 coordination tetrahedron (Tet) from a ditopic ligand, 1, and palladium(II) ions, [PdPy*4]2+ (Py* = 3-chloropyridine), was investigated by a 1H NMR-based quantitative approach (quantitative analysis of self-assembly process, QASAP), which allows one to monitor the average composition of the intermediates not observed by NMR spectroscopy. The self-assembly of Tet takes place mainly through three pathways and about half of the Tet structures were produced through the reaction of a kinetically produced Pd3L6 double-walled triangle (DWT) and 200-nm-sized large intermediates (IntL). In two of the three pathways, the leaving ligand (Py*), which is not a component of Tet, catalytically assisted the self-assembly. Such a multiplicity of the self-assembly process of Tet suggests that molecular self-assembly takes place on an energy landscape like a protein-folding funnel.

Self-Assembly of a Pd4L8 Double-Walled Square Takes Place through Two Kinds of Metastable Species.

The self-assembly process of a Pd4L8 double-walled square (DWS) was investigated. As was seen in Pd2L4 cages, Pd(II)-linked coordination self-assembly processes are generally affected by the rigidity of multitopic ligands. However, the self-assembly of a Pd4L8 DWS from rigid ditopic ligands took place with the formation of two kinds of metastable species [submicrometer-sized species and a Pd3L6 double-walled triangle (DWT)]. This result suggests that the self-assembly process of the DWS is largely affected by the geometry of the final product and not by that of the ditopic ligand.

The Effect of Solvent and Coordination Environment of Metal Source on the Self-Assembly Pathway of a Pd(II)-Mediated Coordination Capsule.

The effect of reaction environment on the self-assembly process of an octahedron-shaped Pd6L8 capsule was investigated. Quantitative analysis of self-assembly process with 1H 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 of the 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.

Self-Assembly Process of Dodecanuclear Pt(II)-Linked Cyclic Hexagon.

The self-assembly process of a Pt(II)-linked hexagonal macrocycle consisting of six linear dinuclear Pt(II) units and six organic ditopic bent ligands was investigated. The process was monitored by (1)H NMR, and the intermediates in the self-assembly were analyzed by the n-k analysis. It was found that a 1:2 complex of a dinuclear Pt(II) unit and an organic ditopic ligand was exclusively observed as an intermediate with a certain lifetime and that the reaction of the 1:2 complex is the rate-determining step in the supramolecular macrocycle formation. The key 1:2 complex was unambiguously characterized by (1)H and DOSY NMR and ESI-TOF mass measurement.

Structural dynamics of overcrowded alkene-based molecular motors during thermal isomerization.

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.

Self-assembly processes of octahedron-shaped Pd6L12 cages.

Self-assembly processes of three octahedron-shaped [Pd6L12]12+ cages were investigated by an NMR-based quantitative approach. As to the on-pathway of the Pd6L12 cage assembly, the final intramolecular ligand exchange in an incomplete cage, [Pd6L12Py*]12+ (Py*: 3-chloropyridine, which was used as a leaving ligand), is the rate-determining step in the self-assembly of all the three [Pd6L12]12+ cages. Contrary to the previous finding that the self-assembly of [PdmL2m]2m+ structures (m = 2, 3) and [Pd6L8]12+ capsules from rigid multitopic ligands efficiently takes place without the formation of kinetically trapped species under mild conditions, in the self-assembly of the [Pd6L12]12+ cages, even relatively rigid ditopic ligands co-produced 100 nm-sized kinetic traps through off-pathways, which would be because the energy landscape becomes more complicated by increasing the number of components in the final assembly. It was found that when Py* was used as a leaving ligand in CD3CN, the [Pd6L12]12+ cages were produced in high yield, preventing the formation of the kinetically trapped species, which indicates that the use of Py* as a leaving ligand in CD3CN is effective to obtain the thermodynamically most stable species.

Temperature-controlled repeatable scrambling and induced-sorting of building blocks between cubic assemblies.

Separation of a homogeneous mixture of different components to reach an ordered out-of-equilibrium state in solution has attracted continuous attention. While this can be achieved using external chemical fuels or photo energy, an alternative energy source is heat. Here we realize a temperature-controlled cycle of transitions between ordered and disordered states based on a mixture of two kinds of building blocks that self-assemble into cubic structures (nanocubes). An almost statistical mixture of nanocubes (disordered state) is thermodynamically most stable at lower temperature (25 °C), while homoleptic assemblies composed of single components are preferentially produced at higher temperature (100 °C) followed by rapid cooling. The scrambling of the building blocks between the nanocubes takes place through the exchange of free building blocks dissociated from the nanocubes. Based on this mechanism, it is possible to accelerate, retard, and perfectly block the scrambling by the guest molecules encapsulated in the nanocubes.

How does chiral self-sorting take place in the formation of homochiral Pd6L8 capsules consisting of cyclotriveratrylene-based chiral tritopic ligands?

The chiral self-sorting process during the self-assembly of homochiral Pd6L8 capsules from cyclotriveratrylene (CTV)-based chiral tritopic ligands (L) and (Py*: 3-chloropyridine) was investigated by an NMR-based approach (QASAP: quantitative analysis of the self-assembly process). From the beginning to the formation of the immature capsules (ICs), enantiomeric ligands are distributed in the intermediates in a non-self-sorting manner, which leads to the isomers of heterochiral ICs over 99% yield. The mismatch of the chirality in the heterochiral ICs prevents intramolecular ligand exchanges in ICs to form the heterochiral capsules. The correction of the chirality in the heterochiral ICs (chiral self-sorting) takes place very slowly to finally lead to the homochiral capsules. The reason why the chiral self-sorting took place in the late stage of the self-assembly (after the formation of the heterochiral ICs) would be due to the relatively high flexibility of the CTV-based ligand.

Two dominant self-assembly pathways to a Pd3L6 double-walled triangle.

An NMR-based quantitative analysis of self-assembly process (QASAP) for the self-assembly of a Pd3L6 double-walled triangle (DWT) from PdPy*4(BF4)2 (Py* indicates 3-chloropyridine) and V-shaped ditopic ligands (L) revealed that DWT was assembled through trinuclear single-walled chains, in which the intramolecular macrocyclization and the formation of double-walls took place leading to the final assembly.

Flexibility of components alters the self-assembly pathway of Pd2L4 coordination cages.

The self-assembly process of a Pd2L4 cage consisting of flexible ditopic ligands and Pd(ii) ions was revealed by QASAP (quantitative analysis of self-assembly process), which enables one to obtain information about the intermediates transiently produced during the self-assembly as the average composition of all the intermediates. It was found that the dominant pathway to the cage is the formation of a submicrometre-sized sheet structure, which was characterized by dynamic light scattering (DLS) and scanning transmission electron microscopy (STEM), followed by the addition of free ditopic ligands to the Pd(ii) centres of the sheet structure to trigger the cage formation. This assembly process is completely different from that of a Pd2L4 cage composed of rigid ditopic ligands, indicating that the flexibility of the components strongly affects the self-assembly process.

Semi-quantitative evaluation of molecular meshing via surface analysis with varying probe radii.

A novel method for the semi-quantitative evaluation of molecular meshing in molecular complexes and assemblies (SAVPR: surface analysis with varying probe radii) is proposed. SAVPR revealed that the extremely high stability of hexameric assemblies (nanocubes) is due to tight molecular meshing between the components in the assemblies, indicating the importance of van der Waals interactions in hydrophobic molecular assemblies.

Induced-fit expansion and contraction of a self-assembled nanocube finely responding to neutral and anionic guests.

Induced-fit or conformational selection is of profound significance in biological regulation. Biological receptors alter their conformation to respond to the shape and electrostatic surfaces of guest molecules. Here we report a water-soluble artificial molecular host that can sensitively respond to the size, shape, and charged state of guest molecules. The molecular host, i.e. nanocube, is an assembled structure consisting of six gear-shaped amphiphiles (GSAs). This nanocube can expand or contract its size upon the encapsulation of neutral and anionic guest molecules with a volume ranging from 74 to 535 Å3 by induced-fit. The responding property of this nanocube, reminiscent of a feature of biological molecules, arises from the fact that the GSAs in the nanocubes are connected to each other only through the hydrophobic effect and very weak intermolecular interactions such as van der Waals and cation-π interactions.