Quantitative Analysis Of Self-assembly Process Research Articles

Coordination Self-Assembly Processes Revealed by Collaboration of Experiment and Theory: Toward Kinetic Control of Molecular Self-Assembly.

The importance of the collaboration of experiment and theory has been proven in many examples in science and technology. Here, such a new example is shown in the investigation of molecular self-assembly process, which is a complicated multi-step chemical reaction occurring in the reaction network composed of a huge number of intermediates. An experimental method, QASAP (quantitative analysis of self-assembly process), developed by us and a numerical approach, NASAP (numerical analysis of self-assembly process), that analyzes the experimental data obtained by QASAP to draw detail molecular self-assembly pathways, which was also developed by us, are introduced, and their application to the investigation of Pd(II)-mediated coordination assemblies are presented. Further, the possibility of the prediction of the outcomes of molecular self-assembly by varying the reaction conditions is also demonstrated. Finally, a future direction in the field of artificial molecular self-assembly based on pathway-dependent self-assembly, that is, kinetic control of molecular self-assembly is discussed.

Towards kinetic control of coordination self-assembly: a case study of a Pd3L6 double-walled triangle to predict the outcomes by a reaction network model.

Numerical analysis of self-assembly process (NASAP) was performed for a [Pd3L6]6+ double-walled triangle (DWT) complex. With a chemical reaction network and a parameter set of the reaction rate constants obtained from a numerical search in an eighteen-dimensional parameter space to obtain a good fit to the data from the experimental counterpart (quantitative analysis of self-assembly process, QASAP), a refined calculation resulted in a detailed time evolution of each molecular species. Analysis based on those clues revealed dominant self-assembly pathways and a balance between inter- and intramolecular reactions, and enabled prediction of the reaction outcomes depending on the initial stoichiometric ratio under kinetic control.

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.

A kinetics study of ligand substitution reaction on dinuclear platinum complexes: Stochastic versus deterministic approach.

The kinetics on a basic ligand substitution reaction on dinuclear platinum complexes [Pt(PEt3 )2 PhPt(PEt3 )2 ]2+ and [Pt(PEt3 )2 PhCOPhPt(PEt3 )2 ]2+ , with the ligands pyridine and 3-chloropyridine, is studied. This is a fundamental step in a self-assembly, and the time evolution has been observed with a new experimental technique, QASAP (quantitative analysis of self-assembly process), which is recently developed by Hiraoka's group. As a result of numerical calculations based on master equation, we succeed in specifying the reaction rate constants with a simple reaction model. In addition, the time evolutions of all the intermediate components produced and consumed in chemical reaction are revealed, including those unobserved in the experiments. The convergence behavior of the existence ratios of specific chemical species calculated with the stochastic algorithm method is compared with those obtained from deterministic formalism based on rate equations, revealing a clear dependence on the number of constituent molecules. © 2018 Wiley Periodicals, Inc.

Chiral self-sorting process\xa0in the self-assembly of homochiral coordination cages from axially chiral ligands

Chiral self-sorting is a phenomenon wherein racemic components are spontaneously sorted into homo- or heterochiral molecular assemblies through chiral discrimination between the components. Chiral self-sorting may be related to biological molecular systems where chiral biomolecules are concerned, but the detail of this sorting process has been unclear. Here we show the chiral self-sorting process in the formation of a homochiral Pd2L4 coordination cage from a racemic mixture of a binaphthol-based ditopic ligand by quantitative analysis of self-assembly process (QASAP). The self-assembly of the cage mainly takes place through two pathways that branch off from the intermolecular reaction of mononuclear complexes. Even though the homochiral cages are thermodynamically the most stable, heterochiral intermediates were preferentially produced at first under kinetic control, which were eventually converted into the homochiral cages. Our results reveal complicated pathways in chiral self-sorting.

Unresolved Issues that Remain in Molecular Self-Assembly

Abstract Two unresolved issues in molecular self-assembly are discussed. Firstly, a novel method for the investigation of molecular self-assembly processes (QASAP: quantitative analysis of self-assembly process) is introduced and recent progress in the understanding of coordination self-assembly processes revealed by QASAP is described. Secondary, a challenge to the construction of discrete molecular self-assemblies that are formed with the aid of weak, nondirectional molecular interactions (such as van der Waals interactions) and the hydrophobic effect is discussed. In the course of the development of hexameric cube-shaped molecular self-assemblies (nanocubes) from gear-shaped amphiphiles (GSAs) in water, a design principle of hydrophobic surface engineering and a novel strategy for the construction of thermally stable discrete assemblies, molecular ‘Hozo’, are presented.

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 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.

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.

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.

Quantitative Analysis of the Self-Assembly Process of a Pd12 L24 Coordination Sphere.

The self-assembly process of a Pd12 L24 sphere was revealed by a quantitative approach (quantitative analysis of self-assembly process: QASAP) quantifying all the substrates, the products, and the observable intermediates, indicating that the Pd12 L24 sphere is produced through several pathways. Firstly, Pdn L2n (n=6, 8, and 9), which are perfectly closed structures smaller than the Pd12 L24 sphere, and a mixture of intermediates not observed by NMR (Int) were produced. Next, the sphere was assembled from intra-/intermolecular reaction of a certain class of Int (path A) and from the coordination of free pyridyl groups in Int to the PdII center of Pdn L2n (n=6, 8, and 9) (path B). While capping the free pyridyl groups in Int with PdII ions perfectly inhibited the sphere formation, the addition of free L to Int accelerated the formation of the sphere.

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.