An ab initio study on nucleic acid bases aromaticities

Cysewski, Piotr

doi:10.1016/j.theochem.2004.10.030

Cited by 85 publications

(80 citation statements)

References 26 publications

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“…The canonical tautomer C2 is less delocalized (HOMED8 0.79) than the C1a and C1b isomers, but it is still aromatic. Similar p-electron delocalization has been previously reported for the canonical tautomer using various measures of aromaticity [70][71][72][73]. The N1 atom in C2 taking the labile proton retains its planarity.…”

Section: Resultssupporting

confidence: 81%

DFT studies on the favored and rare tautomers of neutral and redox cytosine

Raczyńska

Sapuła²,

Zientara‐Rytter³

et al. 2015

Struct Chem

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The complete tautomeric mixture consisting of nine prototropic tautomers has been studied in the gas phase at the DFT(B3LYP)/6-311?G(d,p) level for neutral, oxidized, and reduced cytosine. Rotational isomerism of the exo -OH group and geometrical isomerism of the exo =NH group have also been considered. Tautomeric conversions possible for cytosine have been compared with those for its structural models, 4-amino-and 2-hydroxypyrimidine. Effects of intramolecular interactions between neighboring groups for cytosine are analogous to those observed for model compounds. Although they are not very strong, they are sufficient to influence tautomeric equilibria and relative stabilities of individual tautomers. One-electron oxidation and one-electron reduction change tautomeric preferences. Tautomers that are rare forms for neutral cytosine become favored ones for oxidized and reduced cytosine. Aromaticity is not the main factor that dictates the tautomeric preferences. Stability of functional groups seems to be more important than full electron delocalization.

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Section: Resultssupporting

confidence: 81%

DFT studies on the favored and rare tautomers of neutral and redox cytosine

Raczyńska

Sapuła²,

Zientara‐Rytter³

et al. 2015

Struct Chem

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“…Thus, despite the presence of hydroxyl group attached to C 2 atom no changes in succession of basicities of N 1 and N 3 centers are observed. The same conclusion may be drawn taking into account the results for 8-oxoadenosine and fapy-adenosine [62,63] since protonation takes place predominantly at N 3 position. The gas phase basicities of adenosine analogues were presented in Table 2.…”

Section: Gas Phase Basicitiessupporting

confidence: 58%

“…If nucleosides were considered the simplified model was implemented, which instead of the whole 2'-deoxy-ribose ring, comprised only the methylmethoxy group (-CH 2 -O-CH 3 ) mimicking the N-glycosidic bond. Such model was documented as reliable [60][61][62][63][64][65] for it provides all important features of nucleosides with significant reduction of the size of the studied systems. The results of thermodynamic calculations were critically checked against imaginary frequencies ensuring that the obtained geometries correspond to global minima.…”

Section: Methods Of Calculationsmentioning

confidence: 99%

Molecular Perspective Review of Biochemical Role of Nucleobases Modified by Oxidative Stress

Cysewski¹

2010

CMST

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Numerous damages to cellular DNA are imposed by oxidative stress. Formation of stable products resulting from oxidation of nucleobases is one of many observed consequences. The oxidized species constitute a class of heterocyclic compounds with great diversities of physicochemical properties. Modified nucleosides significantly differ from their canonical protoplasts by tautomeric equilibriums, protolytic properties in the gas phase and water solution, they have altered oxidative susceptibility and N-glycosidic bond stabilities. However, what is most important, they have overwhelmingly altered pairing properties, which are directly responsible for observed cytotoxic properties of these lesions. Besides, since many analogues are structurally different with respect to canonical bases their presence in DNA must impose many energetic, structural and dynamic modifications. These aspect are reviewed as fruits of project no 39 supported by computational grant in Poznań Supercomputing and Networking Center (PSNC, Poland).

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“…?G** method was applied to estimate the diamagnetic ring current intensity on the optimized geometries of diene ring-heterocyclic reactants, products and TSs in the gas phase. Magnetic properties of organic molecules arise from the diamagnetic ring current of aromatic systems [28]. The nucleus independent chemical shift (NICS) is defined as the negative value of the absolute magnetic shielding in centers of rings or 1 Å above or below the molecular plane [29].…”

Section: The Nucleus Independent Chemical Shift (Nics) Studymentioning

confidence: 99%

Control aromaticity in the thermal decomposition of 2,5-dihydrofuran, 2,5-dihydrothiophene and 3-pyrroline: a kinetic and thermodynamic study via DFT

Shiroudi

Zahedi

Zabihi

2010

Reac Kinet Mech Cat

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A theoretical study of the thermal decomposition kinetics of 2,5-dihydrofuran (1), 2,5-dihydrothiophene (2), and 3-pyrroline (3) has been carried out at good agreement with the available experimental values. The nucleus independent chemical shift (NICS) values of all reactants, TSs and products indicate that all studied structures are aromatic and the studied reactions are controlled kinetically and thermodynamically by the change of the aromaticity. Based on the optimized ground state geometries using the MPW1PW91/6-31??G** method, the natural bond orbital analysis (NBO) of donor-acceptor (bonding-antibonding) interactions revealed that by the increase of electronegativity of atom X O; S; NH ð Þ ; LP e ð Þ X1 ! r Ã C 2 ÀH 6 resonance energies and also, the HOMO-LUMO energy-gaps in the ground state structures increase. The results also suggest that in compounds 1-3, the hydrogen elimination are controlled by LP(e) ? r* resonance energies.

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An ab initio study on nucleic acid bases aromaticities

Cited by 85 publications

References 26 publications

DFT studies on the favored and rare tautomers of neutral and redox cytosine

DFT studies on the favored and rare tautomers of neutral and redox cytosine

Molecular Perspective Review of Biochemical Role of Nucleobases Modified by Oxidative Stress

Control aromaticity in the thermal decomposition of 2,5-dihydrofuran, 2,5-dihydrothiophene and 3-pyrroline: a kinetic and thermodynamic study via DFT

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