Helical molecular programming: folding of oligopyridine-dicarboxamides into molecular single helices.

Molecular strands composed of alternating 2,6-diaminopyridine and 2,6-pyridinedicarbonyl units have been designed to self-organize into single stranded helical structures upon forming intramolecular hydrogen bonds. Pentameric strands 11, 12, and 14, heptameric strands 1 and 20, and undecameric strand 15 have been synthesized using stepwise convergent strategies. Single helical conformations have been characterized in the solid state by single crystal X-ray diffraction analysis for four of these compounds. Helices from pentameric strands 12 and 14 extend over one turn, and helices from heptameric 20 and undecameric 15 species extend to one and a half and two and a half turns, respectively. Intramolecular hydrogen bonds are responsible for the strong bending of the strands. 1H NMR shifts both in polar and nonpolar organic solvents indicate intramolecular overlap between the peripheral aromatic groups. Thus, helical conformations also predominate in solution. Molecular stochastic dynamic simulations of strand folding starting from a high energy extended linear conformer show a rapid (600 ps at 300 K) conversion into a stable helical conformation.

Helical molecular programming: supramolecular double helices by dimerization of helical oligopyridine-dicarboxamide strands.

Helically preorganized oligopyridine-dicarboxamide strands are found to undergo dimerization into double helical supramolecular architectures. Dimerization of single helical strands with five or seven pyridine rings has been characterized by NMR and mass spectrometry in various solvent/ temperature conditions. Solution studies and stochastic dynamic simulations consistently show an increasing duplex stability with increasing strand length. The double helical structures of three different dimers was characterized in the solid phase by X-ray diffraction analysis. Both aromatic stacking and hydrogen bonding contribute the double helical arrangement of the oligopyridinedicarboxamide strand. Inter-strand interactions involve extensive face-to-face overlap between aromatic rings, which is not possible in the single helical monomers. Most hydrogen bonds occur within each strand of the duplex and stabilize its helical shape. Some inter-strand hydrogen bonds are found in the crystal structures. Dynamic studies by NMR as well as by molecular modeling computations yield structural and kinetic information on the double helices and on monomer-dimer interconversion. In addition, they reveal the presence of a spring-like extension/compression as well as rotational displacement motions.

Synthesis and functionalization of meso-aryl-substituted corroles.

The Rothemund condensation reaction of pyrrole and aldehydes is an extensively used route to meso-tetraarylporphyrins, but simple modifications of the reaction conditions allow the formation of different macrocycles other than the expected porphyrin. In the presence of an excess of pyrrole, this modified Rothemund approach leads to the synthesis of meso-triary-substituted corroles. This methodology allows the preparation of a wide range of substituted corroles starting from commercially available products. Higher yields have been obtained in the case of benzaldehydes bearing electron-withdrawing substituents, while the reaction fails in the presence of 2,6-disubstituted benzaldehydes. Although if not isolated, some experimental evidences indicate that the linear 5,10,15-triphenylbilane 4 is the precursor of the final corrole ring. Reaction of 5,10,15-triphenylcorrole 2 with an excess of NBS leads to the complete bromination of the macrocycle. Spectroscopic characterization seems to indicate the formation of the porphodimethene-like structure 5, where the macrocyclic aromatic conjugation is interrupted at the 10 position. Metalation of this compound with cobalt acetate and PPh3 affords the corresponding complex. The X-ray crystal structure of triphenylphosphine [2,3,7,8,12,13,17,18-octabromo-5,10,15-tris(4-nitrophenyl)corrolato]- cobalt(III) 8 confirms the ability of corrole ring to retain an almost planar conformation when fully substituted at the peripheral position.

Interconversion of single and double helices formed from synthetic molecular strands.

Synthetic single-helical conformations are quite common, but the formation of double helices based on recognition between the two constituent strands is relatively rare. Known examples include duplex formation through base-pair-specific hydrogen bonding and stacking, as found in nucleic acids and their analogues, and polypeptides composed of amino acids with alternating L and D configurations. Some synthetic polymers and self-assembled fibres have double-helical winding induced by van der Waals interactions. A third mode of non-covalent interaction, coordination of organic ligands to metal ions, can give rise to double, triple and quadruple helices, although in this case the assembly is driven by the coordination geometry of the metal and the structure of the ligands, rather than by direct inter-strand complementarity. Here we describe a family of oligomeric molecules with bent conformations, which exhibit dynamic exchange between single and double molecular helices in solution, through spiral sliding of the synthetic oligomer strands. The bent conformations leading to the helical shape of the molecules result from intramolecular hydrogen bonding within 2'-pyridyl-2-pyridinecarboxamide units, with extensive intermolecular aromatic stacking stabilizing the double-stranded helices that form through dimerization.

Enforced helicity: efficient access to self-organized helical molecular strands by the imine route.

The condensation of the two oligoheterocyclic aldehydes 8 and 16 with the bis-hydrazine 17 gives the bis-hydrazones 1 and 2. These molecular strands are shown to adopt helical conformations of 1.5 and 2.5 turns, respectively. The helical shape of 1 has been confirmed and structurally characterized by X-ray crystallography. The results indicate that the pyrimidine-hydrazone unit is a satisfatory helicity codon, so that the facile hydrazone formation provides an efficient procedure for generating helical structures. This greatly widens the scope of the methodology based on designed heterocyclic sequences for enforcing helicity in molecular strands, and opens interesting routes towards a variety of derived structures.

Adaptive self-assembly: environment-induced formation and reversible switching of polynuclear metallocyclophanes.

Ligand 3 has been shown to self-assemble under coordination of copper(II) cations in a 1:1 ratio in acetonitrile to give equilibrating mixtures of a [2 x 2] grid-type tetranuclear structure 1 and a hexanuclear achitecture of hexagonal shape 2. The latter was confirmed by determination of the crystal structure which further indicated that 2 contained acetonitrile molecules and hydroxo groups bound to the copper(II) centers, which are therefore five-coordinate. The structures assigned to 1 and 2 were further supported by the spectral (mass, UV/Vis) data. The self-assembly process is strongly dependent on the conditions of the medium. An increase in concentration in acetronitrile increases the relative amount of hexamer 2, which appears to be the favored entity at the highest concentrations that can be reached before precipitation occurs. On the other hand, in nitromethane only the tetranuclear complex 1 was detected by mass spectrometry. Replacement of nitromethane by acetonitrile and vice versa indicated the reversible switching between a solution containing either 1 alone or an equilibrium mixture of 1 and 2, respectively. In conclusion, the system described presents several remarkable features: 1) self-assembly with substrate binding, 2) dynamic combinatorial structure generation, and 3) environment-induced structural switching amounting in effect to a process of adaptive self-assembly.