Unexpected Self-Assembly Pathway to a Pd(II) Coordination Square-Based Pyramid and Its Preferential Formation beyond the Boltzmann Distribution

Abstract

Experimental and theoretical investigations of the self-assembly process of a Pd­(II) coordination M6L4 square-based pyramid (SP) were conducted. It was found that the probable self-assembly pathway, in which the dimerization of M2L2 with two M leads to SP, expected from the connectivity of the building blocks is not a major self-assembly pathway to the M6L4 SP. Whether the M6L4 SP is assembled or M2L2 is trapped is determined by an inter- or intramolecular reaction in a chain-like M2L2X, where X is a leaving ligand. The kinetically trapped state where the M6L4 SP is produced from M2L2 beyond the Boltzmann distribution was realized by a concentration-induced process and was kept for at least 2 months at 298 K.

Computational Modeling of Supramolecular Metallo-organic Cages–Challenges and Opportunities

“…NASAP identifies the major assembly pathways using a graph representation and the Gillespie stochastic simulations, 139 and it has been used to probe the formation of [Pd 2 L 4 ] 4+ , 67 , 140 , 141 [Pd 3 L 6 ] 6+ , 142 and [Pd 6 L 4 ] 12+ cages. 138 , 143 , 144 For [Pd 2 L l 4 ] 4+ , 29 intermediate species, 68 elemental reactions, and four pathways were analyzed. 140 Only pathways with small-sized intermediates (M n L m , n ≤ 2 and m ≤ 4) were considered.…”

“…Both QASAP and NASAP have enabled a better understanding of the self-assembly mechanism and, consequently, the rational access to kinetically trapped cages. For example, [Pd 2 L 4 ] 4+ cage 67 and [Pd 6 L 4 ] 12+ square-based pyramid 144 structures have been obtained using this information rather than serendipity. Both methodologies also demonstrated the importance of counteranions in the self-assembly pathway.…”

“…Sato and Hiraoka have also introduced a numerical analysis of the self-assembly process (NASAP), , which complements the QASAP approach by providing information on intermediates at an early stage of self-assembly (<5 min, Figure b). NASAP identifies the major assembly pathways using a graph representation and the Gillespie stochastic simulations, and it has been used to probe the formation of [Pd 2 L 4 ] 4+ , ,, [Pd 3 L 6 ] 6+ , and [Pd 6 L 4 ] 12+ cages. ,, For [Pd 2 L l 4 ] 4+ , 29 intermediate species, 68 elemental reactions, and four pathways were analyzed . Only pathways with small-sized intermediates (M n L m , n ≤ 2 and m ≤ 4) were considered.…”

Kinetically controlled narcissistic self-sorting of Pd(ii)-linked self-assemblies from structurally similar tritopic ligands

“…Previously, NO 3 À and BF 4 À were used for the self-assembly of 2 and a cis-protected Pd(II) complex. [37][38][39][40][41] The [Pd 6 L 4 ] 12+ SP is the dimerized structure of [Pd 2 L 2 ] 4+ (Fig. 4), so the [Pd 2 L 2 ] 4+ units in the [Pd 6 L 4 ] 12+ SP would be stabilized by the counter anion.…”

“…We initially investigated the self-assembly of 1 35,36 and [ Pd Py* 2 ] 2+ in CD 3 NO 2 with different counter anions, PF 6 − or BF 4 − , by monitoring with 1 H NMR spectroscopy. Unlike the self-assembly of 2 with Pd 2+ , which gives the [ Pd 6 2 4 ] 12+ square-base pyramid (SP) or [ Pd 2 2 2 ] 4+ open structure, 37–41 the self-assembly of 1 and [ Pd Py* 2 ](PF 6 ) 2 in a 2 : 3 ratio led to a novel [ Pd 3 1 2 ] 6+ cage, which was characterized by 1 H NMR, 1 H DOSY, and ( H , H )-COSY spectroscopy (Fig. 2a, Fig.…”