Effects of ionization and proton-transfer on bond length alternation in favored and rare isomers of isocytosine

Raczyńska, Ewa D.; Juras, Weronika

doi:10.1016/j.comptc.2018.12.010

Cited by 5 publications

(26 citation statements)

References 58 publications

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“…They exhibit various types of prototropic equilibria (given in Table 1) that originate mainly from the presence of the exo groups, conjugated with the corresponding endo atoms (N and C) [2,4,5]. In the case of pyrimidine bases (U, T, C, and iC) containing one six-membered ring with two endo N atoms and two exo groups (NH 2 and/or OH), two labile protons can move between the conjugated sites according to the analogous scheme of proton-transfers as that given in Figure 1 [28]. For bicyclic purine bases (A and G) and their metabolites (HX, X, and UA) containing the six-membered pyrimidine fragment structurally fused with the five-membered imidazole ring, the imidazole part contains additional labile proton(s) and additional conjugated sites that can also participate in prototropy [29][30][31][32][33][34].…”

Section: Equilibriamentioning

confidence: 89%

On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo

Raczyńska

2023

Molecules

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In this review, the complete tautomeric equilibria are derived for disubstituted pyrimidine nucleic acid bases starting from phenol, aniline, and their model compounds—monosubstituted aromatic azines. The differences in tautomeric preferences for isolated (gaseous) neutral pyrimidine bases and their model compounds are discussed in light of different functional groups, their positions within the six-membered ring, electronic effects, and intramolecular interactions. For the discussion of tautomeric preferences and for the analysis of internal effects, recent quantum-chemical results are taken into account and compared to some experimental ones. For each possible tautomer-rotamer of the title compounds, the bond length alternation, measured by means of the harmonic oscillator model of electron delocalization (HOMED) index, is examined. Significant HOMED similarities exist for mono- and disubstituted derivatives. The lack of parallelism between the geometric (HOMED) and energetic (ΔG) parameters for all possible isomers clearly shows that aromaticity is not the main factor that dictates tautomeric preferences for pyrimidine bases, particularly for uracil and thymine. The effects of one-electron loss (positive ionization) and one-electron gain (negative ionization) on prototropy and bond length alternation are also reviewed for pyrimidine bases and their models.

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Section: Equilibriamentioning

confidence: 89%

On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo

Raczyńska

2023

Molecules

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“…Presence of labile protons leads to existing of nine prototropic tautomers, which are similar to tautomers of other pyrimidine nucleobases. 79,86 When rotational isomerism of exo-OH group and geometrical isomerism of exo N H group are included, 21 tautomers are possible.…”

Section: Isocytosinementioning

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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“…In the case of the HOMED procedure, when the same method is applied for the calculation of R s , R d , R o in the reference compounds and R x in the investigated π-electron systems, computational errors cancel out. Consequently, differences between the HOMED values are lower than 0.05 [21,74].…”

Section: From Linear Tendencies To Scatter Plots Between Rhoma and Homed Indicesmentioning

confidence: 88%

Application of the Extended HOMED (Harmonic Oscillator Model of Aromaticity) Index to Simple and Tautomeric Five-Membered Heteroaromatic Cycles with C, N, O, P, and S Atoms

Raczyńska

2019

Symmetry

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The geometry-based HOMA (Harmonic Oscillator Model of Aromaticity) descriptor, based on the reference compounds of different delocalizations of n- and π-electrons, can be applied to molecules possessing analogous bonds, e.g., only CC, only CN, only CO, etc. For compounds with different heteroatoms and a different number of CC, CX, XX, and XY bonds, its application leads to some discrepancies. For this reason, the structural descriptor was modified and the HOMED (Harmonic Oscillator Model of Electron Delocalization) index defined. In 2010, the HOMED index was parameterized for compounds with C, N and O atoms. For parametrization, the reference molecules of similar delocalizations of n- and π-electrons were employed. In this paper, the HOMED index was extended to compounds containing the CP, CS, NN, NP, PP, NO, NS, PO, and PS bonds. For geometrical optimization of all reference molecules and of all investigated heterocompounds, the same quantum–chemical method {B3LYP/6-311+G(d,p)} was used to eliminate errors of the HOMED estimation. For some tautomeric systems, the Gn methods were also employed to confirm tautomeric preferences. The extended HOMED index was applied to five-membered heterocycles, simple furan and thiophene, and their N and P derivatives as well as for tautomeric pyrrole and phosphole and their N and P derivatives. The effects of additional heteroatom(s) in the ring on the HOMED values for furan are parallel to those for thiophene. For pyrroles, aromaticity dictates the tautomeric preferences. An additional N atom in the ring only slightly affects the HOMED values for the favored and well delocalized NH tautomers. Significant changes take place for their rare CH forms. When intramolecular proton-transfer is considered for phosphole and its P derivatives, the PH tautomers seem to be favored only for 1,2,3-triphosphole/1,2,5-triphosphole and for 1,2,3,5-tetraphosphole. For other phospholes, the CH forms have smaller Gibbs energies than the PH isomers. For phosphazoles, the labile proton in the favored form is linked to the N atom. The PH forms have smaller HOMED indices than the NH tautomers but higher than the CH ones.

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Effects of ionization and proton-transfer on bond length alternation in favored and rare isomers of isocytosine

Cited by 5 publications

References 58 publications

On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo

On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo

Aromaticity of nucleic acid bases

Application of the Extended HOMED (Harmonic Oscillator Model of Aromaticity) Index to Simple and Tautomeric Five-Membered Heteroaromatic Cycles with C, N, O, P, and S Atoms

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