Anions of uracils: N1 or N3? That is the question

Ilyina, Margarita G.; Khamitov, E. M.; Ivanov, S. P.; Мустафин, А. Г.; Хурсан, С. Л.

doi:10.1016/j.comptc.2015.12.024

Cited by 14 publications

(6 citation statements)

References 60 publications

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“…Interesting correlations between HOMA values and stability of anionic forms of different 5,6‐substituted uracil derivatives have been recently reported 82,83 . In the gas phase, the N1 anions are more stable and aromatic than the N3 ones.…”

Section: Aromaticity Of the Nucleic Acid Basesmentioning

confidence: 98%

“…Interesting correlations between HOMA values and stability of anionic forms of different 5,6-substituted uracil derivatives have been recently reported. 82,83 In the gas phase, the N1 anions are more stable and aromatic than the N3 ones. In aqueous solution, the solvent more efficiently stabilizes the more polar N3 anions and aromaticity of N3 anions increases considerably, making both anions almost equally stable.…”

Section: S C H E M Ementioning

confidence: 99%

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Aromaticity of nucleic acid bases

Szatyłowicz

Stasyuk

Solà

et al. 2020

WIREs Comput Mol Sci

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3D shape and the resulting physicochemical properties of double‐helical DNA/RNA structures are determined not only by individual nucleobases, but also by their additive intermolecular interactions. Energetic contribution from aromatic π–π stacking to the stabilization of DNA/RNA is not small and sometimes even comparable to that from H‐bonding. The basis of the stacking interactions lies in the π‐electron structure of individual nucleobases, which can be described by various aromaticity indices. Heteroatoms and exocyclic functional groups make the electronic structure of nucleobases different from aromatic hydrocarbons. Consequently, the cyclic π‐electron delocalization is not the only factor responsible for the relative stability of their tautomers. This review puts the spotlight on interplay between aromaticity of purine and pyrimidine nucleobases and their tautomeric preferences, as well as on the effects of different noncovalent interactions (hydrogen bonding, metal ion coordination, and π–π stacking) on π‐electron delocalization of five‐ and six‐membered rings in individual nucleobases and their complexes. This article is categorized under: Structure and Mechanism > Molecular Structures Electronic Structure Theory > Density Functional Theory

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Section: Aromaticity Of the Nucleic Acid Basesmentioning

confidence: 98%

Section: S C H E M Ementioning

confidence: 99%

Aromaticity of nucleic acid bases

Szatyłowicz

Stasyuk

Solà

et al. 2020

WIREs Comput Mol Sci

View full text Add to dashboard Cite

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“…This has been later supported from density functional theory (DFT) calculations by Hu et al wherein they explained why di‐enol form is hard to detect in aqueous medium. In both uracil and thymine bases, the N1 and N3 sites have similar Gibbs free energies but the presence of water causes increased aromaticity at N3 site leading to more acidic nature of the proton at N3 rather than at N1 . In case of purine bases such as adenine, guanine, xanthine and hypoxanthine, many evidences supports formation and stabilization of anionic species by removal of proton from N7 site rather than N9 ,,.…”

Section: Resultsmentioning

confidence: 99%

Room Temperature Ionic Liquids from Purine and Pyrimidine Nucleobases

et al. 2019

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Purine and pyrimidine nucleobases are of central attraction in biological and chemical sciences as these bases or their derivative are primary components in genetic materials. The solubility of these components is the main concern and puts certain limitations on their use in laboratory synthesis of medicinally important molecules. In this work, efficient conversions of purine and pyrimidine nucleobases (namely uracil, thymine, adenine, guanine, xanthine and hypoxanthine) into corresponding completely water soluble salts are reported. All the reported salts are room temperature ionic liquids except xanthine salts which have melting points higher than 100 °C and hence cannot be called as ionic liquids. Synthesized room temperature ionic liquids from nucleobases were well characterized using spectral and thermal analysis. Experimental data of some physicochemical properties such as density, conductivity, glass transition temperature, melting temperature as well as decomposition temperature reported which shows that the reported ionic liquids are stable upto 200 °C.

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“…The situation is even more complicated if the R5 and/or R6 substituents are prone to undergo the dissociation too. Previously, 12 the relative stability of the N1 and N3 anionic states of diverse uracil derivatives were studied, but the data obtained seem insufficient to rationalize the relations between the uracil structures and their acid−base properties.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Models for Quantitative Description of the Acid–Base Equilibria of the 5,6-Substituted Uracils

et al. 2017

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The acidities of 18 5,6-substituted uracils have been numerically estimated as pK values in terms of three theoretical models. The first scheme includes the calculation of the gas-phase acidity of uracil with the G3MP2B3 method and taking into account the solvent effect using the polarizable continuum approximation PCM(SMD)-TPSS/aug-cc-pVTZ. The second model is one step and implies calculation of the free Gibbs energies of the hydrate complex of uracil (and its anion) with 5 water molecules by the TPSS/aug-cc-pVTZ method. This model accounts for the solvent effect corresponding to both specific and nonspecific solvation. The third scheme required high time and computational resources and includes the strong features of the two previous schemes. Here, the theoretical estimation of pK is performed by the CBS-QB3 composite method. As in the second approach, both specific (as pentahydrate) and nonspecific solvent effects are determined. We have analyzed the advantages and model restrictions of the considered schemes for the pK calculations. All models have systematic errors, which have been corrected with the linear empirical regression relations. In the presented model, the absolute mean deviations of the pK values of uracils dissociating via the N1-H bonds diminish to 0.25, 0.28, and 0.23 pK units (respectively, for I, II, and III models), which corresponds to ∼0.3 kcal/mol on the energy scale. The applicability of our computational schemes to uracils dissociating via N3-H, O-H (orotic acids) and C-H bonds is discussed.

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Anions of uracils: N1 or N3? That is the question

Cited by 14 publications

References 60 publications

Aromaticity of nucleic acid bases

Aromaticity of nucleic acid bases

Room Temperature Ionic Liquids from Purine and Pyrimidine Nucleobases

Theoretical Models for Quantitative Description of the Acid–Base Equilibria of the 5,6-Substituted Uracils

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