Nucleosides as Organizing Architectural Moieties
Authors: Solladie Nathalie 
Published: August 2024

Chemistry “beyond the molecule” is epitomized in nature by a plethora of relatively weak noncovalent interactions. The three-dimensional structures of most biopolymers are controlled with noncovalent interactions, either between different parts of the same strand (as in protein α-helices) or between two separate strands (as in the DNA duplex and protein β-sheet). While nature has refined the construction of biopolymers, our mastery of the subtle noncovalent interactions as synthetic tools is in an early stage of development. Only in the past two decades people begun to develop ways of mimicking the natural light-harvesting complexes by noncovalent assembly of porphyrin units aiming to obtain favored spacing and orientation between the chromophores. The construction of multi-chromophoric assemblies has led to resurgence of interest in coordination chemistry due to formation of ordered arrays directed through molecular recognition events. As a module in the construction of supramolecular assemblies, porphyrins and metallo-porphyrins can be exploited in two different ways: porphyrins can behave as donor building blocks insofar as they comprise meso-substituents, such as pyridyl groups, which can act as ligands that can suitably coordinate to metal cations, while metalloporphyrins can act as acceptor building blocks as soon as the metal atom inside the porphyrin core has at least one axial site available for coordination.
For the last years, we have focussed on cofacial bis-porphyrin tweezers for host/guest interactions and investigated the possibilty to obtain self-coordinated molecular systems with predictable spectral and redox characteristics. We report here the synthesis of a di-nucleotide bearing pendant porphyrins dedicated to adopt a pre-organized coformation with face-to-face porphyrins, and capable to self-organize in a stable sandwich type complexe with bidentate base such as DABCO.1 Using a similar strategy as the one used in antisense research, an artificial nucleotidic backbone was built from modified deoxy-uridine units linked with a more rigid linker than the phosphodiester moieties found in natural oligonucleotides. Antisense research uses modified oligonucleotides, less flexible than natural strands, to pre-organize the system toward the obtaining of stable double helices between synthesized and natural oligonucleotides. A modified oligonucleotidic backbone was here used to target a parallel conformation of the porphyrins appended to each deoxy-uridine moiety. To provide a rigid environment for the porphyrins, the uridine units were coupled in 3’-5’ stepwise fashion using ether-ester type of spacer of suitable length, and porphyrins were anchored to the uridine by means of robust carbon-carbon bonds.
Earlier studies demonstrated that a peptidic linker doesn’t provide sufficient pre-organization to enhance significantly the association constant with bidentate bases such as DABCO on the contrary of some flexible linkers such as uridine or 2’-deoxyuridine. We document herein that the gain in stability for the formation of sandwich type host-guest complex with DABCO can be even greater when a dinucleotide linker is used. Such pre-organization increases the association constants by one to two orders of magnitude when compared to the association constants of the same bidentate ligands with a reference Zn(II) porphyrin. Comparison of these results with those obtained for rigid tweezers shows a better efficiency of the flexible nucleosidic dimers.
We thus document the fact that the choice of rigid spacers is not the only way to pre-organize bis-porphyrins, and that some well-chosen nucleosidic linkers offer an interesting option for the synthesis of such devices. Furthermore, the chirality and enantio-purity of the nucleosidic linkers paves the way toward the selective complexation of enantio-pure bidentate guests and the resolution of racemates.

Acknowledgements

This work was supported by the CNRS and the French Ministry of Research.

References

Solladié, R. Rein, S. Bouatra, S. Merkas, C. Sooambar, I. Piantanida, M. Žinić, J. Porphyrins Phthalocyanines
2020, 24, 636-645.