Exploration of the polymorphic solid-state landscape of an amide-linked organic cage using computation and automation

Organic cages can possess complex, functionalised internal cavities that make them promising candidates for synthetic enzyme mimics. Conformationally flexible but chemically robust structures are needed for adaptable guest binding and catalysis, but these rapidly exchanging systems are difficult to resolve in solution. Here, we use inexpensive calculations and high-throughput crystallisation experiments to identify accessible cage conformations for a recently reported organic cage by ‘locking’ them in the solid state. The conformers identified exhibit a range of distances between the carboxylic acid groups in the internal cavity, suggesting adaptability towards binding a wide array of target guest molecules. The complexity of the observed crystal structures goes beyond what is possible with state-of-the-art crystal structure prediction

Ester-Based Synthetic Information Oligomers

Nature has long inspired chemists to replicate the molecules produced by evolution. Arguably, the most important of these are the nucleic acids because of the ability to store and transfer information through duplex formation using Watson-Crick base pairing. Biochemists have prepared modified DNA analogues, in which the phosphate diester units used for synthesis, the bases used for recognition, and the sugar backbones have all been replaced. These systems have been found to form stable duplexes, so it is clear that the precise structure of these three modules is not crucial for information manipulation through a sequence-selective duplex formation. This non-uniqueness of the structure of the nucleic acids with respect to their function provides a challenge for synthetic chemists to design information molecules capable of directed evolution. A range of oligomeric and polymeric materials has been reported that are capable of duplex-formation and site-specific recognition, but few functional materials based on a sequence of supramolecular interactions are known. Herein, we present efforts towards a new family of oligomers that contain a sequence of hydrogen-bonding recognition sites, used as the bits for binary data encoded in an organic information molecule. Several monomer designs were implemented and investigated, and the final system uses single-point hydrogen bond recognition motifs between electron-deficient phenols (D) and electron-rich phosphine oxides (A), which provide strong interactions in non-polar solvents (K$_{A·D}$ ≈ 4000 M$^{−1}$ in toluene). Ester chemistry was employed for the synthesis of the corresponding homo- and heterodimers, exploiting the robustness of the ester bonds and the ease of their synthesis. A trifluoromethyl group incorporated into the structure of D enhanced the strength of the hydrogen bonds and provided a convenient probe to study the association through $^{19}$F NMR spectroscopy. The strongly hydrogen-bonding recognition motifs were observed to cooperatively form sequence-complementary duplexes with high fidelity and without substantial intramolecular folding. Those promising results led to the investigation of supramolecular behaviour of longer oligomers. An ADAD tetrame was successfully synthesised and its molecular structure was elucidated. Supramolecular association of the ADAD 4-mer was investigated through NMR spectroscopy and the results suggest that the room temperature ADAD exists as a stem-loop that further assembles in a manner akin to kissing interactions of single-stranded nucleic acids. These results lay strong foundations for the future development of new functional materials based on synthetic information molecules