Quantum Mechanical Analysis of Nonenzymatic Nucleotidyl Transfer Reactions: Kinetic and Thermodynamic Effects of β–γ Bridging Groups of dNTP Substrates

Rate (k) and equilibrium (K) constants for the reaction of tetrahydrofuranol with a series of Mg(2+) complexes of methyl triphosphate analogues, CH3O-P(O2)-O-P(O2)-X-PO3(4-), X = O, CH2, CHCH3, C(CH3)2, CFCH3, CHF, CHCl, CHBr, CFCl, CF2, CCl2, and CBr2, forming phosphate diester and pyrophosphate or bisphosphonate in aqueous solution were evaluated by B3LYP/TZVP//HF/6-31G* quantum chemical calculations and Langevin dipoles and polarized continuum solvation models. The calculated log k and log K values were found to depend linearly on the experimental pKa4 of the conjugate acid of the corresponding pyrophosphate or bisphosphonate leaving group. The calculated slopes of these Brønsted linear free energy relationships were βlg = -0.89 and βeq = -0.93, respectively. The studied compounds also followed the linear relationship Δlog k = 0.8Δlog K, which became less steep, Δlog k = 0.6Δlog K, after the range of studied compounds was extended to include analogues that were doubly protonated on γ-phosphate, CH3O-P(O2)-O-P(O2)-X-PO3H2(2-). The scissile Pα-Olg bond length in studied methyl triphosphate analogues slightly increases with decreasing pKa of the leaving group; concomitantly, the CH3OPα(O2) moiety becomes more positive. These structural effects indicate that substituents with low pKa can facilitate both Pα-Olg bond breaking and the Pα-Onuc bond forming process, thus explaining the large negative βlg calculated for the transition state geometry that has significantly longer Pα-Onuc distance than the Pα-Olg distance.