Multiple Metal Binding to the 9-Methyladenine Model Nucleobase Involving N1, N6, and N7: Discrete Di- and Trinuclear Species with Different Combinations of Monofunctional PdII and PtII Entities

The exocyclic amino group of adenine in PtII and PdII complexes: a critical comparison of the X-ray crystallographic structural data and gas phase calculations

A detailed computational (DFT level of theory) study regarding the nature of the exocyclic amino group, N6H₂, of the model nucleobase 9-methyladenine (9MeA) and its protonated (9MeAH⁺) and deprotonated forms (9MeA_-H), free and metal-complexed, has been conducted. The metals are Pt^II and Pd^II, bonded to nitrogen-containing co-ligands (NH₃, dien, bpy), with N1, N6, and N7 being the metal-binding sites, individually or in different combinations. The results obtained from gas phase calculations are critically compared with X-ray crystallography data, whenever possible. In the majority of cases, there is good qualitative agreement between calculated and experimentally determined C6-N6 bond lengths, but calculated values always show a trend to larger values, by 0.02-0.08 Å. Both methods indicate, with few exceptions, a high degree of double-bond character of C6-N6, consistent with an essentially sp²-hybridized N6 atom. The shortest values for C6-N6 distances in X-ray crystal structures are around 1.30 Å. Exceptions refer to cases in which DFT calculations suggest the existence of a hydrogen bond with N6H₂ acting as a H bond acceptor, hence a situation with N6 having undergone a substantial hybridization shift toward sp³. Nevertheless, even in these cases the C6-N6 bond (1.392 Å) is still halfway between a typical C-N single bond (1.48 Å) and a typical C=N double bond (1.28 Å). This scenario is, however, not borne out by X-ray crystallographic results, and is attributed to the absence of counter anions and solvent molecules in the calculated structures.

Purinyl N(3)-Directed Palladium-Catalyzed C-H Alkoxylation of N(9)-Arylpurines: A Late-Stage Strategy to Synthesize N(9)-(ortho-Alkoxyl)arylpurines

A palladium-catalyzed alkoxylation of N(9)-arylpurines with primary or secondary alcohols has been developed successfully, which is a rare C-H activation reaction of polynitrogenated purines and offers a late-stage strategy to synthesize N(9)-(ortho-alkoxyl)arylpurines. Although there are more than four nitrogen atoms present in the purine moiety, the reaction can be effectively conducted by sterically blocking the N(1) site for catalyst coordination and first employing the purinyl N(3) atom as a directing group.

The challenge of deciphering linkage isomers in mixtures of oligomeric complexes derived from 9-methyladenine and trans-(NH3)2Pt(II) units

Metal coordination to N9-substituted adenines, such as the model nucleobase 9-methyladenine (9MeA), under neutral or weakly acidic pH conditions in water preferably occurs at N1 and/or N7. This leads, not only to mononuclear linkage isomers with N1 or N7 binding, but also to species that involve both N1 and N7 metal binding in the form of dinuclear or oligomeric species. Application of a trans-(NH3)2Pt(II) unit and restriction of metal coordination to the N1 and N7 sites and the size of the oligomer to four metal entities generates over 50 possible isomers, which display different feasible connectivities. Slowly interconverting rotamers are not included in this number. Based on (1)H NMR spectroscopic analysis, a qualitative assessment of the spectroscopic features of N1,N7-bridged species was attempted. By studying the solution behavior of selected isolated and structurally characterized compounds, such as trans-[PtCl(9MeA-N7)(NH3)2]ClO4⋅2H2O or trans,trans-[{PtCl(NH3)2}2(9MeA-N1,N7)][ClO4]2⋅H2O, and also by application of a 9MeA complex with an (NH3)3Pt(II) entity at N7, [Pt(9MeA-N7)(NH3)3][NO3]2, which blocks further cross-link formation at the N7 site, basic NMR spectroscopic signatures of N1,N7-bridged Pt(II) complexes were identified. Among others, the trinuclear complex trans-[Pt(NH3)2{μ-(N1-9MeA-N7)Pt(NH3)3}2][ClO4]6⋅2H2O was crystallized and its rotational isomerism in aqueous solution was studied by NMR spectroscopy and DFT calculations. Interestingly, simultaneous Pt(II) coordination to N1 and N7 acidifies the exocyclic amino group of the two 9MeA ligands sufficiently to permit replacement of one proton each by a bridging heterometal ion, Hg(II) or Cu(II), under mild conditions in water.