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Pathway selection in the self-assembly of Rh₄L₄ coordination squares under kinetic control.

ABSTRACT: Pathway selection principles in reversible reaction networks such as molecular self-assembly have not been established yet, because achieving kinetic control in reversible reaction networks is more complicated than in irreversible ones. In this study, we discovered that coordination squares consisting of cis-protected dinuclear rhodium(II) corner complexes and linear ditopic ligands are assembled under kinetic control, perfectly preventing the corresponding triangles, by modulating their energy landscapes with a weak monotopic carboxylate ligand (2,6-dichlorobenzoate: dcb^-) as the leaving ligand. Experimental and numerical approaches revealed the self-assembly pathway where the cyclization step to form the triangular complex is blocked by dcb^-. It was also found that one of the molecular squares assembled into a dimeric structure owing to the solvophobic effect, which was characterized by nuclear magnetic resonance spectroscopy and single-crystal X-ray analysis.

SUBMITTER: Okazawa A

PROVIDER: S-EPMC10651846 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Pathway selection in the self-assembly of Rh<sub>4</sub>L<sub>4</sub> coordination squares under kinetic control.

Okazawa Atsushi A Sanada Naoki N Takahashi Satoshi S Sato Hirofumi H Hiraoka Shuichi S

Communications chemistry 20231115 1

Pathway selection principles in reversible reaction networks such as molecular self-assembly have not been established yet, because achieving kinetic control in reversible reaction networks is more complicated than in irreversible ones. In this study, we discovered that coordination squares consisting of cis-protected dinuclear rhodium(II) corner complexes and linear ditopic ligands are assembled under kinetic control, perfectly preventing the corresponding triangles, by modulating their energy ...[more]

PMID: 37968322

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Project description:The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium 'RNA reactor' enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world.

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Pathway selection in the self-assembly of Rh₄L₄ coordination squares under kinetic control.

Publications

Pathway selection in the self-assembly of Rh<sub>4</sub>L<sub>4</sub> coordination squares under kinetic control.

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Pathway selection in the self-assembly of Rh4L4 coordination squares under kinetic control.

Publications

Pathway selection in the self-assembly of Rh<sub>4</sub>L<sub>4</sub> coordination squares under kinetic control.

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OmicsDI is part of the ELIXIR infrastructure

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Pathway selection in the self-assembly of Rh₄L₄ coordination squares under kinetic control.