Guanidinium Promoted Cleavage of Phosphoric Diesters: Kinetic Investigations and Calculations Provide Indications on the Operating Mechanism

The catalytic activity of the guanidinium units toward the cleavage of phosphoric diesters is deeply investigated both with kinetic experiments and DFT calculations. The first part of the investigation aims to determine how the structure of the substrate (phenyl or alkyl esters) is able to influence the guanidinium-catalyzed hydrolysis changing the mechanism from A_ND_N to A_N+D_N. In the cleavage of the DNA model bis­(4-nitrophenyl)­phospate (BNPP), experimental kinetic data highlight the operation of a guanidine–guanidinium catalytic dyad that can act both intermolecularly and intramolecularly on different molecular scaffolds exhibiting notable values of effective molarity. ³¹P NMR spectra and DFT investigation provide indication that the deprotonated guanidine involved in such a catalysis acts as a general base in the deprotonation of a water molecule involved in the cleavage, and not as nucleophilic unit. Moreover, DFT calculations were carried out to determine the guanidinium promoted activation energy of pseudorotation. The results indicate a remarkable drop in the activation energy of this process for dialkylphosphate esters explaining, in part, the higher sensitivity of diribonucleoside to the presence of guanidinium-based catalysts compared to the more activated RNA model HPNP.