Catalysis Effects of Water Molecules and of Charge on Intramolecular Proton Transfer of Uracil

Abstract

In this work, the three most stable uracil isomers (U1, U2, and U3) and their neutral, positive, and negative charged multihydrates are chosen as research objects to investigate the tautomeric process between the most stable uracil, U1, and its two minor stable isomers, U2 and U3. By the study, deeper insight can be obtained regarding point mutations induced by uracil deformation. Toward the target, the activation energies of the intramolecular proton transfer (tautomeric process) as well as the catalysis effects of water molecules and of charges attached are investigated using density functional theory (DFT) calculations by means of the B3LYP exchange and correlation functions. Results reveal that water molecules hold a stronger catalysis effect on the proton transfer in these negative charged uracil hydrates than in the neutral counterparts. The optimal number of water molecules needed to catalyze the proton transfer is determined as two in the neutral hydrated systems, whereas it is three in the negative charged systems. Positive charge attachment, however, hinders the intramolecualr proton transfer of uracil, and the charge and the proton of uracil will transfer to the water clusters if water molecules are attached. Then the positive charged hydrates look more like U1a/b+[(H2O)n+H+] species in structure. Analysis reveals that it is the acceptance process of the last proton to determine the impossibility of proton transfer and result in the failure of tautomeric processes from cat-U1a-nw to cat-U2-nw and from cat-U1b-nw to cat-U3-nw. Detailed structural parameters and energy changes are discussed for the above different processes.

Mechanism of the Isotopic Exchange Reaction of the 5‐H Hydrogen of Uracil Derivatives in Water and Nonprotic Solvents

“…Although it was possible to converge this calculation, it did not yield a single-proton TS. These findings are in agreement with previous studies on the mechanism of the keto-enol tautomerism of nucleic acid bases, [19,[44][45][46] pyridine derivatives, [38][39][40][41] and other compounds [43,51] in aqueous media. It was found that the tautomerization reactions proceed preferentially by a multiple proton-transfer mechanism with the assistance of two to three water molecules.…”

“…First, the canonical diketo form of uracil is changed to a keto-enol form (3,4-U), which is a fast stepwise process. [19,47,50] The 3,4-U form is then transformed into the rare 3,5-U tautomer. The organic solvents could act as catalysts in the formation of this rare tautomer.…”

“…Water can act as a bifunctional catalyst, that is, it can accept a proton from the donor site of the solute molecule and transfer a different proton to the acceptor site on the solute. [19,[38][39][40][41][42][43][44][45][46] On the other hand, the available data on the kinetics of the keto-enol tautomerism of carbonyl compounds in aprotic solvents are scarce. [47] Results and Discussion…”

CO2 capture and gas separation on boron carbon nanotubes

“…Based on the optimized structures at DFT-D level, the author calculate the wavefunctions at the B3LYP/6-311+G(d) level of theory, then AIM theory which has been used to successfully determine intermolecular interactions of different systems is used in these systems. [30][31][32][33][34][35][36][37][38][39] In the AIM analyses, The transition state between chemisorption and physisorption of CO 2 have been investigated using the complete LST (linear synchronous transit)/QST (quadratic synchronous transit) method 41 implemented in DMOL3 code. The electron distribution and transfer mechanism are determined using the Mulliken method.…”

Isotope exchange reactions of the hydrogen H-5 of selected pyrimidine derivatives and the preparation of tritium-labeled pyrimidines

“…We suggested the following mechanism of isotopic exchange (Scheme 2): The exchange reaction involves a very rare uracil tautomer, which has an sp 3 hybridized carbon atom in position 5. First, the canonical diketo form of uracil is changed to a ketoenol form (3,4-U), which is a fast stepwise process [27][28][29] . The 3,4-U form is then transformed to the rare 3,5-U tautomer.…”