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

Abstract

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 AD to A+D. 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. P 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.

Phosphodiester models for cleavage of nucleic acids

“…The dianionic phosphorane ( I 2− ) is very unstable and cannot pseudorotate, owing to the high barrier for transfer of negatively charged oxygen from equatorial to apical position. Recent DFT calculations suggest the barrier to be about 30 kcal mol −1 [ 27 ].…”

“…In this technique, rate constants are determined as a function of isotopic ratio n , and the shape of a plot k n / k o vs n gives information on the proton transfer processes. Unfortunately, interpretation of the data is not always straightforward, owing to possible contribution of the equilibrium isotope effect that refers to binding of the catalyst to the phosphate group [ 27 , 38 ].…”

Conformational Mobility and Efficiency in Supramolecular Catalysis. A Computational Approach to Evaluate the Performances of Enzyme Mimics

“…namely whenever there are covalent bonds forming or breaking. [47,52] About the present case, on the basis of the results of this series of in silico experiments, we believe data in Table 1, carried out with the mere PCM method, are more effective for the study of the reaction mechanism.…”

“…[46] The ground state structures considered in the present investigation consists in catalyst-substrate complex held together by an electrostatic and a chelate double hydrogen bonding interaction in which the guanidinium unit interacts with the phosphate group of the substrate. [36,37,47] The ground state optimizations have been used in the QST3 procedure for the transition state searches and to evaluate the activation energy of the process (vide infra). For the cleavage of HPNP, the frequency calculations of the optimized TS structures (see Figure 1 and Supporting Information), show a single imaginary frequency.…”

Multivalent and Multifunctional Calixarenes in Bionanotechnology

“…A high degree of cooperation between the catalytic groups in 38a,b (up to three orders of magnitude compared with the background hydrolysis) was observed with the 1,3-distal guanidinocalixarene 38a slightly more effective than the 1,2-vicinal regioisomer 38b. [107][108][109][110] Interestingly, by increasing the number of guanidinium groups, and therefore the positive charges at the upper rim, it is possible to obtain a tetraguanidinium derivative 38c that, upon monodeprotonation, is able to efficiently cleave ATP into ADP and phosphate. In this case, the rate enhancement is due to a combination of neutral guanidine (nucleophilic catalysis) and protonated guanidinium units which bind the substrate, activate it and stabilise the leaving group.…”