The preferred sites for the benzylation of adenine under basic conditions were proven to be the N9 and N3 positions. Formation of the N9‐benzyladenine product is favored in polar aprotic solvents, such as DMSO, whereas the proportion of N3‐benzyladenine formed increases as the proportion of polar protic solvents, such as water, increases. X‐ray crystal structures were obtained for both N9‐benzyladenine and N3‐benzyladenine. 1H‐13C HMBC NMR spectroscopy revealed diagnostic correlations used to assign the 1H and 13C NMR chemical shifts confirming that the solution structures in three different solvents were the same as the isolated crystals. 13C NMR assignment for N9‐benzyladenine, N3‐benzyladenine, and N7‐benzyladenine was confirmed by computation using ADF.

The adeninate anion (Ade−) is a useful nucleophile used in the synthesis of many prodrugs (including those for HIV AIDS treatment). It exists as a contact ion-pair (CIP) with Na+ and K+ (M+) but the site of coordination is not obvious from spectroscopic data. Herein, a molecular-wide and electron density-based (MOWED) computational approach implemented in the implicit solvation model showed a strong preference for bidentate ion coordination at the N3 and N9 atoms. The N3N9-CIP has (i) the strongest inter-ionic interaction, by −30 kcal mol−1, with a significant (10–15%) covalent contribution, (ii) the most stabilized bonding framework for Ade−, and (iii) displays the largest ion-induced polarization of Ade−, rendering the N3 and N9 the most negative and, hence, most nucleophilic atoms. Alkylation of the adeninate anion at these two positions can therefore be readily explained when the metal coordinated complex is considered as the nucleophile. The addition of explicit DMSO solvent molecules did not change the trend in most nucleophilic N-atoms of Ade− for the in-plane M-Ade complexes in M-Ade-(DMSO)4 molecular systems. MOWED-based studies of the strength and nature of interactions between DMSO solvent molecules and counter ions and Ade− revealed an interesting and unexpected chemistry of intermolecular chemical bonding.

Rare anionic forms of nucleic acids play a significant biological role and lead to spontaneous mutations and replication and translational errors. There is a lack of information surrounding the stability and reactivity of these forms. Ion pairs of monosodium and -potassium salts of adenine exist in DMSO solution with possible cation coordination sites at the N1, N7 and N9 atoms of the purine ring. At increasing concentrations π-π stacked dimers are the predominant species of aggregates followed by higher order aggregation governed by coordination to metal cations in which the type of counter ion present has a central role in the aggregate formation.

The alkylation of adenine using alkyl halides under basic conditions in dimethyl sulfoxide (DMSO), a common reaction to achieve N9‐alkylated adenine derivatives, is often low yielding with unreacted adenine and complicated reaction mixtures. Herein, we report the reaction monitoring of the alkylation of adenine in DMSO in the presence of NaH using benzylic halides via real‐time 1H NMR spectroscopy. NMR analysis revealed that under these generally used reaction conditions, the adeninate anion starting material is protonated as the anionic nucleophile abstracts a labile proton from an alkoxy sulfonium ion intermediate formed via the Kornblum oxidation reaction. To prevent the protonation of the adeninate anion, the reaction was performed in the presence of a mop‐up base DBU. Simultaneously increasing the concentration of the alkyl halide and the mop‐up base in a 1:1 ratio resulted in a complete reaction; however, increasing the temperature of the reaction promoted depletion of the starting material by protonation and hence reduced conversion to products. This result implies that heating of such electrophiles in DMSO should be avoided. The addition of a mop‐up base can help resolve the complication of protonation arising from the Kornblum oxidation reaction in alkylation reactions under similar conditions.