Structures, stabilities and tautomerizations of uracil and diphosphouracil tautomers

Jalbout, Abraham F.; Trzaskowski, Bartosz; Xia, Yuanzhi; Li, Y.; Hu, Xingbang; Li, H.; El‐Nahas, Ahmed M.; Adamowicz, Ludwik

doi:10.1016/j.chemphys.2006.10.026

Cited by 27 publications

(13 citation statements)

References 55 publications

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“…In addition, structural studies of uracil and all its tautomeric forms have been developed by different levels of theoretical approximations [8][9][10][11] as ab initio methods or semi-empirical correlations (with different basis sets), arriving in all cases to the conclusion that the dioxo form is, by far, the most stable one. 12 The dioxo structure is completely in accordance with Watson-Crick model of RNA, in which uracil in uridine must take its dioxo tautomeric form in order to be totally complementary with the normal amino tautomeric structure of adenosine. However, fluorescence excitation studies showed the coexistence of the most stable form and keto-enol tautomers, giving strong evidence about the possibility of having this kind of tautomerism involved and taking part at the moment of replication.…”

Section: Introductionmentioning

confidence: 76%

Tautomerism of uracil and related compounds: A mass spectrometry study

Colasurdo

Pila

Iglesias

et al. 2017

Eur J Mass Spectrom (Chichester)

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It has been demonstrated that uracil has a preponderant tautomeric form, but it is also known that different tautomers co-exist in this equilibrium. In this work, mass spectrometry is used as a helpful tool to analyse the equilibria, using derivative compounds to forbid the presence of some tautomers and ion trap mass spectrometry to follow relevant fragmentation pathways. Theoretical calculations were performed to confirm tautomers abundance by energy minimization in gas phase. Analysis of mass spectra of uracil, three methyl-substituted uracils, 2-thiouracil and three benzouracils suggest that uracil exists mainly as three tautomers in gas phase: one major structure that corresponds to the classical structure of uracil (pyrimidine-2,4(1H,3H)-dione) bearing two carbonyls and two NH moieties, and two minor enolic forms (4-hydroxypyrimidin-2(1H)-one and 2-hydroxypyrimidin-4(1H)-one). Such tautomeric distribution is supported by theoretical calculations, which show that they are the three most stable tautomers.

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Section: Introductionmentioning

confidence: 76%

Tautomerism of uracil and related compounds: A mass spectrometry study

Colasurdo

Pila

Iglesias

et al. 2017

Eur J Mass Spectrom (Chichester)

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“…It is the least aromatic nucleobase with NICS = −1.2 ppm and HOMA6 = 0.5. Important to note that its most stable tautomer with two carbonyl groups is energetically more stable than all other tautomers by >10 kcal/mol, as shown in Table 3 78 . The most favorable tautomers of uracil are presented in Scheme 3.…”

Section: Aromaticity Of the Nucleic Acid Basesmentioning

confidence: 97%

“…Important to note that its most stable tautomer with two carbonyl groups is energetically more stable than all other tautomers by >10 kcal/mol, as shown in Table 3. 78 The most favorable tautomers of uracil are presented in Scheme 3. For u1, the lone electron pair of each nitrogen atom is n-π cross-conjugated with π-electrons of the ring and exo-C O group.…”

Section: Uracilmentioning

confidence: 99%

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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“…Therefore, it is reasonable to employ B3LYP/6-311G* as a practical tool for modeling molecular structures and computing energetic data of Se-containing molecules studied in this work. This forecast can also be supported by the initiative that for small organic systems B3LYP method can give more reliable results than higher level ab initio methods [65][66][67][68][69]. In addition, density functional theory (DFT) calculations (1), where X = F, Cl, Br, CH 3 , OCH 3 , CF 3 , CN, and NH 2 ; Y = Me, Et, and i-Pr have been applied successfully to a number of problems in chalcogen-nitrogen chemistry [70][71][72][73][74].…”

Section: Resultsmentioning

confidence: 95%

On the selenepin/benzene selenide valence tautomerizations: electronic and steric effects at theoretical levels

2009

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Tautomerization in selenepin (1) benzene selenide (2) binary system is found to favor, 2, at HF, MP2, and B3LYP levels, using 6-311G* basis set. Electronic effects appear to have small effects on 1 2 equilibria and show little impact on the conformational ring inversions of 1, at the same levels. In contrast, steric effects effectively decrease DH values in an order inversely proportional to the size of the substituents employed (Me [ Et [ i-Pr). A possible Se extrusion is suggested to be the main reason why no 2 has ever been detected experimentally.

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Structures, stabilities and tautomerizations of uracil and diphosphouracil tautomers

Cited by 27 publications

References 55 publications

Tautomerism of uracil and related compounds: A mass spectrometry study

Tautomerism of uracil and related compounds: A mass spectrometry study

Aromaticity of nucleic acid bases

On the selenepin/benzene selenide valence tautomerizations: electronic and steric effects at theoretical levels

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