A theoretical study on tautomerization processes of dehydrated and monohydrated cytosine

Mazzuca, Donatella; Marino, Tiziana; Russo, Nino; Toscano, Marirosa

doi:10.1016/j.theochem.2007.02.026

Cited by 29 publications

(44 citation statements)

References 23 publications

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“…Our DFT calculations are in good agreement with those reported in the literature [39-42, 47, 49]. However, it should be mentioned here that the percentage contents of major and minor forms depend on the level of calculations [38][39][40][41][42][43][44][45][46][47][48][49][50] as well as on the experimental method applied [30][31][32][33][34][35][36]. For example, the DFT methods predict the canonical tautomer C2 as the favored form for neutral cytosine, whereas the HF, MPn and CC methods indicate the C1a isomer.…”

Section: Resultssupporting

confidence: 90%

“…The common conclusion on its major tautomers (C2 and C1a) in the gas phase has not yet been formulated. The microhydration by one, two, or three water molecules [42,45,46] and the macrohydration by using the continuum models [40,41,45,48,49] favor the 'canonical' tautomer C2.…”

Section: Resultsmentioning

confidence: 99%

“…In aqueous solution, two tautomeric forms of cytosine (C2 and C3) seem to dominate [37]. Unfortunately, the complete tautomeric mixture of cytosine has not been investigated by quantum chemical methods [38][39][40][41][42][43][44][45][46][47][48][49][50]. Maximum six tautomers have been studied for neutral cytosine (C1-C3, C5, C6, and C8), and the amide-iminol and amine-imine conversions analyzed [40][41][42].…”

Section: Tautomermentioning

confidence: 99%

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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: 90%

Section: Resultsmentioning

confidence: 99%

Section: Tautomermentioning

confidence: 99%

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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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“…Forthe binding site A,keto-Cy·H 2 O is predicted to be more stable than enol-Cy·H 2 Oby3kJ mol À1 at the G4MP2 and CCSD(T)/aug-cc-pVTZ levels.U nlike in the case of Cy monomer,w eb elieve that structural relaxations occur rapidly in Cy·(H 2 O) n during expansion because of the following reasons.1 )T automerization barriers in Cy· (H 2 O) 1-3 are greatly reduced with the assistance of water bridges to 40 kJ mol À1 (see the Supporting Information) or less. [23,24,[39][40][41][42] 2) Isomerization barriers between different water binding sites are expected to be even lower. For example,i th as been shown that the barrier between two remote H-bonding sites of the t-formanilide·H 2 Oc omplex is only about 12 kJ mol À1 .…”

mentioning

confidence: 99%

Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence

Yen

Shi

et al. 2015

Angew Chem Int Ed

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Ultrafast excited-state deactivation dynamics of small cytosine (Cy) and 1-methylcytosine (1mCy) microhydrates, Cy⋅(H2O)1-3 and 1mCy⋅(H2O)1,2, produced in a supersonic expansion have been studied by mass-selected femtosecond pump-probe photoionization spectroscopy at about 267 nm excitation. The seeded supersonic expansion of Ar/H2O gas mixtures allowed an extensive structural relaxation of Cy and 1mCy microhydrates to low-energy isomers. With the aid of electronic structure calculations, we assigned the observed ultrafast dynamics to the dominant microhydrate isomers of the amino-keto tautomer of Cy and 1mCy. Excited-state lifetimes of Cy⋅(H2O)1-3 measured here are 0.2-0.5 ps. Comparisons of the Cy⋅H2O and 1mCy⋅H2O transients suggest that monohydration at the amino Watson-Crick site induces a substantially stronger effect than at the sugar-edge site in accelerating excited-state deactivation of Cy.

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“…Vibrational properties of such species were investigated at the harmonic level from a solvent discrete model containing up to five water molecules with the B3LYP model chemistry25–28.…”

Section: Introductionmentioning

confidence: 99%

Vibrational analysis beyond the harmonicity from Ab initio molecular dynamics: Case of cytosine in its anhydrous and aqueous forms

Carbonnière

Thicoipe

Very

et al. 2012

Int J of Quantum Chemistry

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This study provides the set of theoretical anharmonic fundamental transitions for cytosine in its anhydrous and hydrated forms from a vibrational analysis issuing from a time-dependent approach. This evaluation is compared to the time-independent VPT2 approach and to the experimental data available in the literature for the two forms. To investigate the vibrational property of a solute in a polar protic solvent, that is, the aqueous form of cytosine in this particular case, a practicable computational strategy to properly take into account the solvent effect is proposed. This is done by considering a combination of polarizable continuum model and of discrete solvent molecules model. The number of solvent molecules was chosen in such a way that the solute-solvent complex presents only one dominant stable conformer at 298 K. The quality of this combined solvent model is illustrated by comparing the structural and anharmonic vibrational properties achieved with those obtained from a purely implicit and purely explicit solvent model. Structural optimizations, harmonic frequencies, and anharmonic frequencies issuing from the VPT2 evaluation [33] were performed with the Gaussian09 program [34]. Electronic structure calculations were performed at the DFT level using CARBONNIERE ET AL.

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A theoretical study on tautomerization processes of dehydrated and monohydrated cytosine

Cited by 29 publications

References 23 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

Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence

Vibrational analysis beyond the harmonicity from Ab initio molecular dynamics: Case of cytosine in its anhydrous and aqueous forms

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