Conformational flexibility of di- and tetrahydropyrimidine rings in nucleic acid bases. An ab initio study

Шишкин, Олег В.

doi:10.1016/s0022-2860(98)00303-2

Cited by 34 publications

(7 citation statements)

References 23 publications

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“…Depending on the contribution in the tautomeric mixture, individual tautomers can be considered as major (10% < x < 100%), minor (0.1% < x < 10%), or rare forms ( x < 0.1%). The major and minor isomers can be detected experimentally by various spectroscopic techniques, some of them already applied to nucleobases ,− and also to neutral isocytosine. ,,, However, the rare forms possible in the isomeric mixture can only be investigated theoretically. ,,,,,− ,− ,− ,− ,− Quantum-chemical methods applied to all possible isomers of tautomeric system give complete information on tautomeric conversions and on amounts of each isomer in the tautomeric mixture. This kind of information is not accessible on the basis of experimental spectroscopic investigations, particularly for short-lived charged radicals.…”

Section: Resultsmentioning

confidence: 99%

“…For neutral isocytosine, a change of tautomeric preferences has already been discovered when proceeding from the gas phase to aqueous solution and in the solid state. ,,,,− For investigations, various spectroscopic techniques and quantum-chemical calculations have been applied and the following conclusions reported. The isomer iC3 (Figure ), possessing the canonical tautomeric functions like for G in DNA or RNA (Figure S1 (SI)), is favored in aqueous solution, whereas the isomer iC1 , corresponding to the rare form G *, predominates in the gas phase or apolar environment.…”

Section: Introductionmentioning

confidence: 99%

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Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Raczyńska

Makowski

2018

J. Phys. Chem. A

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Intramolecular proton-transfers (prototropic conversions) have been studied for the guanine building block isocytosine (iC), and effects of positive ionization, called one-electron oxidation (iC - e → iC), and negative ionization, called one-electron reduction (iC + e → iC), on tautomeric conversions when proceeding from neutral to ionized isocytosine have been discussed. Although radical cations and radical anions are very short-lived species, the ionization effects could be investigated by quantum-chemical methods. Such kind of studies gives some information about the labile protons and the most basic positions in the neutral and radical forms of the tautomeric system. For investigations, the complete isomeric mixture of isocytosine has been considered and calculations performed in two extreme environments, apolar {DFT(B3LYP)/6-311+G(d,p)} and polar {PCM(water)//DFT(B3LYP)/6-311+G(d,p)}. For selected isomers, the G4 theory has also been applied. There are no good relations for energetic parameters of neutral and ionized forms. Ionization energies depend on localization of labile protons. Tautomeric equilibria for neutral and ionized isocytosine, favored sites of protonation and deprotonation, and favored structures of protonated and deprotonated forms strongly depend on environment. Acidity of iC is close to that of the iC conjugate acid, and basicity of iC is close to that of the iC conjugate base. This increase of acid-base properties of charged radicals explains the proton-transfer in ionized pairs of nucleobases. When compared to other pyrimidine bases such as uracil (U) and cytosine (C), which exhibit analogous tautomeric equilibria between nine prototropic tautomers as isocytosine, the tautomeric preferences for iC, iC, iC, U, U, U, C, C, and C are completely different. The differences suggest that acid-base properties of functional groups, their stabilities, and ionization energies play a principal role in proton-transfers for pyrimidine bases and influence compositions of tautomeric mixtures.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Raczyńska

Makowski

2018

J. Phys. Chem. A

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“…It has been known for quite a time that (hyper)-aromaticity can be maintained even in systems deviating profoundly from planarity ( 58–62 ). QM calculations suggest that NA bases possess a notable degree of conformational flexibility despite their aromatic character ( 32–37 ). The transition of the heterocycle from a planar equilibrium geometry to a nonplanar structure with an endocyclic torsion angle of ±20° results in an energy increase of <2.8 kcal/mol ( 34 ).…”

Section: Discussionmentioning

confidence: 99%

“…The assumption of rigid, planar bases is also reflected in the direct interpretational schemes for the three-bond scalar coupling ( 3 J) across the glycosidic bond ( 24 , 25 ), residual dipolar couplings (RDCs) ( 26 ) and auto- and cross-correlated relaxation rates ( 27–30 ). Recent quantum chemical (QM) calculations, however, suggest that all NA bases are highly flexible molecules and possess a nonplanar effective conformation ( 31–38 ). Nonetheless, the direct experimental evidence for NA base nonplanarity has been missing.…”

Section: Introductionmentioning

confidence: 99%

Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion

Sychrovský

Foldynová-Trantírková

Špačková

et al. 2009

Nucleic Acids Research

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We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides—it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations.

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“…The recent study of the conformational flexibility by Shishkin demonstrated that the molecules of uracil and thymine are not conformationally rigid due to nonaromatic and antiaromatic characters of the cyclic π-systems in these molecules. This feature is relevant to the formation of covalent anions of these molecules since, as mentioned, the out-of-plane distortion occurs when an excess electron attaches to their valence shells.…”

Section: Introductionmentioning

confidence: 99%

Isomerism of the Covalent Anion of the Uracil−Thymine Dimer. Ab Initio Study

1999

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Theoretical ab initio calculations have been performed to determine the ability of the uracil-thymine (U‚T) dimer to form stable covalent anions. The are two major conclusions of this work (i) Two isomeric structures of the covalent U‚T dimer have been found in the calculations. The anion, where the excess electron is located at the uracil molecule, is 1.4 kcal/mol more stable than the form where the excess electron is located at the thymine molecule. (ii) The ring of the molecule where the excess electron is localized in noticeably nonplanar.

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Conformational flexibility of di- and tetrahydropyrimidine rings in nucleic acid bases. An ab initio study

Cited by 34 publications

References 23 publications

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion

Isomerism of the Covalent Anion of the Uracil−Thymine Dimer. Ab Initio Study

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