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

Abstract

A detailed computational (DFT level of theory) study regarding the nature of the exocyclic amino group, N6H, of the model nucleobase 9-methyladenine (9MeA) and its protonated (9MeAH) and deprotonated forms (9MeA), free and metal-complexed, has been conducted. The metals are Pt and Pd, bonded to nitrogen-containing co-ligands (NH, 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 sp-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 N6H acting as a H bond acceptor, hence a situation with N6 having undergone a substantial hybridization shift toward sp. 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.

Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair

“…The NH2 group of A8 changes its hybridization from a sp 2 -like planar state to a sp 3 -like tetrahedral state, with Hg1 acting as the fourth binding partner. Such a hybridization shift of the exocyclic amino group of adenine has been reported before in structurally characterized metal complexes [89]. The NN pattern can be identified after 0.6 ps, corresponding to the situation in Figure 13a.…”

Mapping H+ in the Nanoscale (A2C4)2-Ag8 Fluorophore

“…54 First, their lone pairs are delocalized into the aromatic nucleobases, as these amines are sp 2 hybridized with short, double-bond C−N bond lengths and planar NH 2 geometries. 55,56 Second, these groups are expected to be fully protonated at neutral pH because their pK a ∼ 18. 57,58 Despite these impediments, X-ray diffraction shows that the silvers are anchored at these sites (Figure 1D).…”

“…In contrast, the exocyclic C6-NH 2 of adenine and the C4-NH 2 of cytosine are expected to be poor Lewis bases for two reasons . First, their lone pairs are delocalized into the aromatic nucleobases, as these amines are sp 2 hybridized with short, double-bond C–N bond lengths and planar NH 2 geometries. , Second, these groups are expected to be fully protonated at neutral pH because their p K a ∼ 18. , Despite these impediments, X-ray diffraction shows that the silvers are anchored at these sites (Figure D). Most importantly, NSLD maps suggest that the C6-NH 2 and C4-NH 2 coordinate silvers because they are singly deprotonated (see Table and the Supporting Information).…”