Differential reactivity of α and β 2′-deoxyribonucleosides towards protonation and metalation

Metal‐Ion‐Mediated Base Pairs in Nucleic Acids

“…To confirm independently the differential reactivity of the anomers towards protonation and to investigate the underlying reasons, density functional theory (DFT) calculations at the B3LYP/6-311+G** level were performed using 1,2,4-triazole nucleoside 2 as an example. [52] The result of these calculations is in very good agreement with the experimental data [∆pK a = 0.16 vs. 0.21 (7)]. Interestingly, no significant differences in the charge distribution between sugar moiety and nucleobase were observed between the two anomers, ruling out different charge localizations as a reason for the different acidity.…”

“…Artificial nucleosides for metal-ion-mediated base pairs in DNA (R = 2Ј-deoxyribose). The nucleobases are a) imidazole 1; [49] b) 1,2,4-triazole 2; [49,51,52] c) tetrazole 3; [49,53] d) benzimidazole 4; [52] e) 1H-imidazo [4,5-b]pyridine 5; [52] f) 3H-imidazo [4,5-b]pyridine (1-deazapurine) 6; [48,52] g) 7-amino-3H-imidazo [4,5-b]pyridine (1-deazaadenine) 7; [50] h) 5-methyl-2,2Ј-bipyridine 8; [54,66,67] i) 2,2Ј-bipyridine; [68] j) 4-(pyridin-2-yl)pyrimidin-2-one; [69] k) ophenylenediamine; [41] l) catechol; [55] m) 2-aminophenol; [56] n) pyridine; [57,[61][62][63][64]71,72] o) 3-hydroxy-2-methyl-4-pyridone; [58][59][60] p) R = OH: pyridine-2,6-dicarboxylic acid; [61,62] R = NH 2 : pyridine-2,6-dicarboxamide; [64] R = NHCH 3 : N,NЈ-dimethylpyridine-2,6-dicarboxamide; [64] q) 2,6-bis(methylsulfanylmethyl)pyridine; [63] r) 8-hydroxyquinoline; [65] s) 6-(pyridin-2-yl)purine; [70] t) salicylaldehyde; [60,[73][74][75] u) 4-(2,2Ј-bipyridin-6-yl)pyrimidin-2-one; …”

“…pK a values of protonated artificial 2Ј-deoxyribonucleosides. [48,49,52] Nucleoside α anomer [a] β anomer [a] ∆pK a (α -β)…”

“…Therefore, the nucleosides were titrated with increasing amounts of metal ion solutions, and the chemical shifts of their aromatic protons were followed by 1 H NMR spectroscopy. [49,52] Individual formation constants were calculated from the experimental data by using the computer program EQNMR. [118] Table 3 provides a list of these stability constants.…”

Synthesis and AcidBase Properties of an Imidazole‐Containing Nucleotide Analog, 1‐(2′‐Deoxy‐β‐D‐ribofuranosyl)imidazole 5′‐Monophosphate (dImMP2−)

“…g ) In analogy to Entry 4, based on the pK a value of H(dRibBzIm) þ as determined by 1 H-NMR spectroscopy at natural ionic strength (4.21 AE 0.03) [32], the same value is estimated to amount to 4.29 AE 0.06 at I ¼ 0.1m.…”