Facile and Selective Electrostatic Stabilization of Uracil N(1)- Anion by a Proximate Protonated Amine: A Chemical Implication for Why Uracil N(1) Is Chosen for Glycosylation Site

Abstract

A question of how uracil nitrogen N(1) is selectively activated in enzymes (e.g., for deglycosylation in uracil-DNA glycosylase) has been utterly overlooked, to which we have addressed by a model study with 6-((1,4,7,10-tetraazacyclododecyl)methyl)uracil (HL, cyclen-attached uracil). The uracil N(1)H of the diprotonated cyclen-attached uracil (HL·2H+) is easily deprotonated to be N(1)- anion form (L-·2H+) in aqueous solution. The deprotonation constant (pKa) of 7.14 for HL·2H+ ⇄ L-·2H+ + H+ was determined by potentiometric pH titration at 25 °C with I = 0.10 (NaClO4). The unusually low deprotonation constant (cf. pKa = 9.9 for 3-methyluracil) is due to the electrostatic stabilization of the N(1)- anion by a proximate secondary ammonium cation of the diprotonated cyclen at physiological pH. The X-ray crystal structure of HL·2H+ as its dipicrate revealed that the uracil N(1)H is linked by a hydrogen bond network to one of the cyclen secondary ammonium cation through a water. Crystals of HL·2H+·(picrate)2·H2O (C25H32N12O17) are triclinic, space group P1̄ (no. 2) with a = 9.295(4) Å, b = 19.67(1) Å, c = 8.886(6) Å, α = 94.36(3)°, β = 102.95(4)°, γ = 87.04(4)°, V = 1576(8) Å3, Z = 2, R = 0.054, and Rw = 0.081. The electrostatic stabilization of uracil N(1)- anion is reassessed by a comparative study with a zinc(II) complex with the cyclen-attached uracil, where Zn2+ in the cyclen cavity strongly binds to the uracil N(1)- (localized) anion. The deprotonation of N(1)H of HL (1 mM) occurred below pH 5 by the effect of equimolar Zn2+, a stronger acid than two protons. Crystals of the zinc(II) complex (C13H23N6O2Zn·ClO4·H2O) are triclinic, space group P1̄ (no. 2) with a = 9.461(3) Å, b = 13.156(4) Å, c = 8.687(2) Å, α = 101.21(2)°, β = 103.55(2)°, γ = 73.21(2)°, V = 997(0) Å3, Z = 2, R = 0.063, and Rw = 0.093. For comparison, we also have investigated the uracil N(1) acidity with an ethylenediamine-attached uracil and an isomeric cyclen-attached (at C(5)) uracil. The present example of electrostatic stabilization of N(1)- anion may explain the facile uracil N(1)-alkyl (e.g., glycosyl) bond formation and cleavage in enzymes.