Dipole moments of 2,4-diketopyrimidines

Kulakowska, I.; Geller, Maciej; Lesyng, Bogdan; Wierzchowski, K.L.

doi:10.1016/0005-2787(74)90339-6

Cited by 84 publications

(36 citation statements)

References 17 publications

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“…Their values are, respectively, -40.9 and -13.6°in aT n1 c5 , 13.8 and 0.5°in aT can val , and -40.7 and -4.8°in aT n3 c5 . In consequence of these distortions, the energy of the corresponding neutrals increases by 28 The effect of hydration on the stability of valence anions was studied at the B3LYP/6-31++G** level within the PCM model with fully optimized geometries (Table 4). As expected from the electrostatic model, all five anionic tautomers become adiabatically bound with respect to the neutral nT can , with the stability always exceeding 1.8 eV.…”

Section: Mp2mentioning

confidence: 99%

On the Unusual Stability of Valence Anions of Thymine Based on Very Rare Tautomers: A Computational Study

et al. 2006

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We characterized anionic states of thymine using various electronic structure methods, with the most accurate results obtained at the CCSD(T)/aug-cc-pVDZ level of theory followed by extrapolations to complete basis set limits. We found that the most stable anion in the gas phase is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion, aT(c5)(nl), is characterized by an electron vertical detachment energy (VDE) of 1251 meV and it is adiabatically stable with respect to the canonical neutral nT(can) by 2.4 kcal/mol. It is also more stable than the dipole-bound (aT(dbs)(can)), and valence anion aT(val)(can) of the canonical tautomer. The VDE values for aT(dbs)(can)and T(val)(can) are 55 and 457 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2458 meV has a proton transferred from N3H to C5 aT(c5)(n3). It is less stable than aT(val)(can) by 3.3 kcal/mol. The mechanism of formation of anionic tautomers with the carbons C5 or C6 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of the anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Within the PCM hydration model, the low-lying valence anions become adiabatically bound with respect to the canonical neutral; becomes the most stable, being followed by aT(c5)(nl), aT(c5)(n3), aT(can), and aT(c5)(nl).

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Section: Mp2mentioning

confidence: 99%

On the Unusual Stability of Valence Anions of Thymine Based on Very Rare Tautomers: A Computational Study

et al. 2006

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“…For a C base, the calculated dipole moment is the largest one and is 7.04 D. The dipole moment of a G base is slightly smaller (6.98 D). The T base has an even smaller dipole moment (4.74 D), and the A base is the least polar base with 54 respectively. Depending on the basis set, the MP2 calculated 44 dipole moments of C, G, T, and A bases are 6.27-6.49, 6.45-6.65, 4.01-4.31, and 2.55-2.56 D, respectively.…”

Section: Dna Base Molecules Distant From the Cu(111) Surfacementioning

confidence: 99%

Electronic Properties of DNA Base Molecules Adsorbed on a Metallic Surface

et al. 2007

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The internal electronic structure of single deoxyribonucleic acid (DNA) base molecules (i.e., guanine, adenine, cytosine, and thymine) adsorbed on a metallic surface of Cu (111) is determined in detail using density functional theory (DFT) computations. In contrast to the intuitive beliefs that a molecule weakly interacts with a substrate and its electronic structure is only slightly perturbed, our simulations reveal strong hybridizations and interactions between molecular and metallic states. Stipulated by the symmetries of a base molecule and the Cu(111) surface, oxygen atoms of a base approach close to the substrate, breaking the parallel orientation of the π-system with respect to the surface. Such a behavior is the most pronounced for one oxygen containing bases, leading to the chemisorption of cytosine and guanine and to stronger hybridization of their electronic states with metallic ones. Oxygen free adenine, on the other hand, lies nearly flat on a Cu substrate and interacts weakly with the surface through physisorption. The calculated local electron density of states spectra demonstrate the absence of pure localized molecular states for all four DNA bases, yet they show the smallest delocalization for adenine and thymine and the largest for guanine and cytosine. The observed diversity of the geometrical and electronic structures of the nucleobases on the Cu substrate provides guidelines for interpreting DNA tunneling spectra in the scanning tunneling microscopy (STM) measurements. Our results open a new prospective for understanding biomolecule adsorbates and have an important implication for a possible differentiation of nucleotide sequences in DNA through STM.

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“…In order to extend our knowledge of radiationinduced damage in biomolecular systems and provide relevant parameters for radiation-based biomedical applications, it is necessary to apply these models to increasingly more complicated biomolecules. It is important to note that the great majority of the molecules of biological interest have a considerably high permanent dipole moment, for example, H 2 O [10], the DNA and RNA bases [11][12][13], tetrahydrofuran * g.garcia@iff.csic.es (THF) [14], and the target molecule of the present study pyrimidine [15].…”

Section: Introductionmentioning

confidence: 99%

Cross-section calculations for positron scattering from pyrimidine over an energy range from 0.1 to 10000 eV

et al. 2013

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We report a computational investigation of positron scattering by pyrimidine (C 4 H 4 N 2 ) in the gas phase. Integral and differential cross sections have been calculated over a broad energy range by employing two distinct ab initio quantum scattering methods: the R-matrix method and a corrected form of the independent-atom representation, at low and high energies, respectively. Since pyrimidine is a strong polar molecule further dipole-induced excitations have been calculated in the framework of the first Born approximation. Good agreement is found between the different computational models and fair agreement is found with prior experimental results.

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Dipole moments of 2,4-diketopyrimidines

Cited by 84 publications

References 17 publications

On the Unusual Stability of Valence Anions of Thymine Based on Very Rare Tautomers: A Computational Study

On the Unusual Stability of Valence Anions of Thymine Based on Very Rare Tautomers: A Computational Study

Electronic Properties of DNA Base Molecules Adsorbed on a Metallic Surface

Cross-section calculations for positron scattering from pyrimidine over an energy range from 0.1 to 10000 eV

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