The ribosome builds proteins by joining together amino acids in an order determined by messenger RNA. Here, we report on the design, synthesis, and operation of an artificial small-molecule machine that travels along a molecular strand, picking up amino acids that block its path, to synthesize a peptide in a sequence-specific manner. The chemical structure is based on a rotaxane, a molecular ring threaded onto a molecular axle. The ring carries a thiolate group that iteratively removes amino acids in order from the strand and transfers them to a peptide-elongation site through native chemical ligation. The synthesis is demonstrated with ~10(18) molecular machines acting in parallel; this process generates milligram quantities of a peptide with a single sequence confirmed by tandem mass spectrometry.

We report on an improved strategy for the preparation of artificial molecular machines that can pick up and assemble reactive groups in sequence by traveling along a track. In the new approach a preformed rotaxane synthon is attached to the end of an otherwise fully formed strand of building blocks. This "rotaxane-capping" protocol is significantly more efficient than the "final-step-threading" method employed previously and enables the synthesis of threaded molecular machines that operate on extended oligomer, and potentially polymer, tracks. The methodology is exemplified through the preparation of a machine that adds four amino acid building blocks from a strand in sequence, featuring up to 20-membered ring native chemical ligation transition states.

We report on the active template synthesis of a [2]rotaxane through a Goldberg copper-catalyzed C-N bond forming reaction. A C2-symmetric cyclohexyldiamine macrocycle directs the assembly of the rotaxane, which can subsequently serve as a ligand for enantioselective nickel-catalyzed conjugate addition reactions. Rotaxanes are a previously unexplored ligand architecture for asymmetric catalysis. We find that the rotaxane gives improved enantioselectivity compared to a noninterlocked ligand, at the expense of longer reaction times.

We report on the use of the hydrogen bond acceptor properties of some phosphorus-containing functional groups for the assembly of a series of [2]rotaxanes. Phosphinamides, and the homologous thio- and selenophosphinamides, act as hydrogen bond acceptors that, in conjunction with an appropriately positioned amide group on the thread, direct the assembly of amide-based macrocycles around the axle to form rotaxanes in up to 60% yields. Employing solely phosphorus-based functional groups as the hydrogen bond accepting groups on the thread, a bis(phosphinamide) template and a phosphine oxide-phosphinamide template afforded the corresponding rotaxanes in 18 and 15% yields, respectively. X-ray crystallography of the rotaxanes shows the presence of up to four intercomponent hydrogen bonds between the amide groups of the macrocycle and various hydrogen bond accepting groups on the thread, including rare examples of amide-to-phosphinamide, -thiophosphinamide, and -selenophosphinamide groups. With a phosphine oxide-phosphinamide thread, the solid-state structure of the rotaxane is remarkable, featuring no direct intercomponent hydrogen bonds but rather a hydrogen bond network involving water molecules that bridge the H-bonding groups of the macrocycle and thread through bifurcated hydrogen bonds. The incorporation of phosphorus-based functional groups into rotaxanes may prove useful for the development of molecular shuttles in which the macrocycle can be used to hinder or expose binding ligating sites for metal-based catalysts.

The synthesis of 5,5'-dibromo-2,2'-bipyridine and 5-bromo-2,2'-bipyridine, useful intermediates for elaboration into more complex ligands through metal-catalyzed coupling reactions, can be efficiently conducted on a multigram scale from inexpensive starting materials. The described procedure is reliably scalable and suitable for the synthesis of tens of grams of 5,5'-dibromo-2,2'-bipyridine. 5-Bromo-2,2'-bipyridine is produced as a minor product. The 5,5'-disubstituted-2,2'-bipyridine motif has excellent coordination properties and is a versatile building block for the synthesis of functional materials (including biodiagnostics, photovoltaics and organic light-emitting diodes) and complex molecular topologies (including catenanes and trefoil and pentafoil knots). The selective stepwise functionalization of 5,5'-dibromo-2,2'-bipyridine by consecutive Stille couplings is therefore illustrated and documented in detail. The synthesis of 5,5'-dibromo-2,2'-bipyridine takes 4-5 d: 1 d to prepare the key intermediate 2,2'-bipyridine dihydrobromide, 3 d for its reaction with bromine in a steel bomb reaction vessel and 8 h to isolate and purify the final product.