Metal-promoted synthesis of amidines containing the model nucleobases 1-methylcytosine and 9-methyladenine

From cyclic amines and acetonitrile to amidine zinc(ii) complexes

A seemingly simple combination of [Zn(quin)₂(H₂O)] (quin⁻ = quinaldinate) and a selected secondary cyclic amine, piperidine (pipe), pyrrolidine (pyro) or morpholine (morph), afforded in acetonitrile a number of products: anionic homoleptic quinaldinate, neutral heteroleptic quinaldinate/amine and quinaldinate/amidine complexes. The piperidine and pyrrolidine systems underwent reaction with acetonitrile to give amidines. The in situ formed piperidinoacetamidine (pipeam) or pyrrolidinoacetamidine (pyroam) coordinated to zinc(ii). Reactions with piperidine led to trans-[Zn(quin)₂(pipe)₂]·2CH₃CN (1), [Zn(quin)₂(pipe)]·cis-[Zn(quin)₂(pipe)₂] (2), pipeH[Zn(quin)₃]·CH₃CN (3), [Zn(quin)₂(pipeam)]·CH₃CN (4a), [Zn(quin)₂(pipeam)]·2CHCl₃ (4b), pipeamH[Zn(quin)₃] (5) and pipeamH[Zn(quin)₂(CH₃COO)]·acetamide (6) (pipeH⁺ and pipeamH⁺ denote protonated amine or amidine). By analogy, [Zn(quin)₂(pyro)₂] (7), pyroH[Zn(quin)₃]·CH₃CN (8), pyroH[Zn(quin)₂Cl] (9), [Zn(quin)₂(pyroam)]·CH₃CN·0.5pyroam·0.5H₂O (10a), [Zn(quin)₂(pyroam)]·2CHCl₃ (10b), [Zn(quin)₂(pyroam)]·CH₂Cl₂ (10c) and pyroamH[Zn(quin)₃] (11) were obtained in the pyrrolidine reactions. The morpholine system allowed isolation of only two novel products, trans-[Zn(quin)₂(morph)₂] (12) and morphH[Zn(quin)₃]·CH₃CN (13). Importantly, no amidine could be isolated. Instead, in autoclaves at 105 °C morpholine degraded to ammonia, as confirmed by mass spectrometry of the gas phase. pyroamH[Zn(quin)₃] exists in two polymorphs which differ in the binding modes of quinaldinate ligands. In 11triclinic, the metal ion of [Zn(quin)₃]⁻ features a five-coordinate environment, whereas that in 11monoclinic is surrounded by six donors. Stabilities of the [Zn(quin)₃]⁻ isomers were assessed with DFT calculations. The one with a six-coordinate zinc(ii) ion was found to be more stable than its five-coordinate counterpart. Favorable intermolecular interactions in the solid state stabilize both and reduce the energy difference between them. The calculations show the conversion of the five-coordinate [Zn(quin)₃]⁻ into its coordinatively saturated isomer to be an almost barrierless process.

Piperidine and pyrrolidine, both belonging to a group of secondary cyclic amines, reacted with acetonitrile in the presence of zinc(ii) to give the corresponding amidines that coordinated to the metal through their imine nitrogen.