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Phosphoryl‐Transfer Reaction in RNA under Alkaline Conditions
Author(s) -
AcostaSilva Carles,
Bertran Joan,
Branchadell Vicenç,
Oliva Antoni
Publication year - 2018
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201802332
Subject(s) - chemistry , solvent , catalysis , dielectric , solvent effects , reaction rate constant , electric field , enzyme catalysis , reaction mechanism , ribozyme , reaction rate , computational chemistry , rna , organic chemistry , kinetics , materials science , biochemistry , physics , optoelectronics , quantum mechanics , gene
Abstract The phosphoryl‐transfer reaction in RNA under alkaline conditions by exploring the influence of several solvents theoretically was studied. The calculations were carried out by using the M06‐2X functional and the solvents were taken as a continuum by using the solvent model density (SMD) method. The main findings show that the O2′‐P‐O5′ angle in the reactants, the free activation energies, and the reaction mechanism are clearly dependent on the dielectric constant of the environment, thus showing that the electrostatic term is the determining factor for this chemical system with two negative charges. Our study seems to indicate that water, the solvent with the greatest dielectric constant, would be the solvent that increases the reaction rate the most. As this outcome was not the case in enzymatic catalysis, one has to conclude that, in the case of proteins as well as for ribozymes, the enzymatic catalysis is not mainly due to the solvent reaction field, but to local electrical fields as a result of enzyme preorganization.