Nucleic acid bases studied by matrix isolation vibrational spectroscopy: Uracil and deuterated uracils

Barnes, Austin J.; Stuckey, M.A.; Gall, L. Le

doi:10.1016/0584-8539(84)80073-2

Cited by 122 publications

(153 citation statements)

References 27 publications

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“…The NH and CH stretching modes usually appear in the region 3,000-3,200 cm −1 with the N 1 H, N 3 H and C 6 H stretching modes at higher frequencies, in accordance with the values reported in [3,6,26,[57][58][59]. The Raman band spectrum shows two strong band peaks at 3,180 and 3,125 cm −1 for the N 1 H and N 3 H stretching modes, respectively, and also one C 6 H stretching mode appears with a peak band of intermediate strength at 3,065 cm −1 , which are given in Table 1, and are in good agreement with [45].…”

Section: Nh/ch Modessupporting

confidence: 77%

“…The γ (C=O) modes have been proposed near 430 cm −1 [17,20]. In contrast, other studies [26,32,45,58] have proposed the region 680-+ 820 cm −1 for these modes, a result supported by the studies from my laboratory. For 5-amionuracil, these bands are observed with very strong peaks at 795 and 768 cm −1 and have been correlated to the two γ (C 2 =O 7 ) and γ (C 4 =O 8 ) modes.…”

Section: C=o Modescontrasting

confidence: 39%

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FTIR and Raman Spectra Compared with Ab Initio Calculated Frequency Modes for 5-Aminouracil

Singh

2008

J Biol Phys

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Infrared (IR) and Raman spectra of 5-aminouracil were recorded in the region 200-4,000 cm −1 . Assuming under the C s point group that the distribution of the normal mode of vibrations between the two species are planar (a ) and non-planar (a ), given by 25a + 11a of which 30 modes (21a + 9a ) correspond to the uracil moiety and six modes (4a + 2a ) correspond to the NH 2 group, with a comparison of theoretically ab initio calculated frequencies, the results are in reasonably good agreement with the experimental IR and Raman spectra. Consistent assignments have been made for the internal modes of the NH 2 group, especially for the anti-symmetric NH 2 stretching and bending modes. The nonequivalence of the two NH bonds of the NH 2 group suggests a difference in the strength of the two hydrogen bonds on the pyrimidine ring. Symmetry and anti-symmetry NH stretching modes of the NH 2 group show the invalidity of the empirical relationship. These two NH 2 stretching frequencies are distinctly separated from the CH/NH ring stretching frequencies. A strong and sharp IR band that acts at 3,380 cm −1 could be identified as the anti-symmetric NH 2 mode whereas the band at 3,290 cm −1 smaller density could be identified as the symmetric NH 2 stretching mode.

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Section: Nh/ch Modessupporting

confidence: 77%

Section: C=o Modescontrasting

confidence: 39%

FTIR and Raman Spectra Compared with Ab Initio Calculated Frequency Modes for 5-Aminouracil

Singh

2008

J Biol Phys

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“…First, the vibrational levels associated with the N 1 -D stretch, 0.322 eV [10], are reduced relative to those of N 1 -H, 0.432 eV. Thus, the positions of the VFRs relative to the barrier indicated schematically in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Uracil, deuterated at the N 1 and N 3 positions, was produced by standard methods [10]. The 1 H NMR spectrum indicated that the purity of the sample was 92 ± 5%.…”

Section: Resultsmentioning

confidence: 99%

Dissociative electron attachment to uracil deuterated at the N1 and N3 positions

Scheer

Silvernail

Belot

et al. 2005

Chemical Physics Letters

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“…The U1 dioxo tautomer has been reported as the most stable tautomeric form of uracil in the gas phase [28,29]. The presence in the gas phase of the 3H-0x0-hydroxyl tautomer (U2) has also been reported [30], with an estimated relative energy of 40 kJ/mol.…”

Section: Uracil Tautomersmentioning

confidence: 96%

Solvent effects in density functional calculations of uracil and cytosine tautomerism

Paglieri

Corongiu

Estrin

1995

Int J of Quantum Chemistry

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mThe effects of the solvent on the tautomeric equilibria of cytosine and uracil are studied using Onsager's reaction field model in the framework of density functional theory. In this model, the solute molecule is placed in a spherical cavity of radius a, immersed in a continuous medium with a dielectric constant E , treating the solute-solvent electrostatic interactions at the dipole level. The cavity radius is evaluated by determining the molecular volume with a quantum mechanical approach. The solvent effect brings significant changes in the geometrical parameters of some cytosine tautomers, but only very small changes to those of the uracil tautomers. Our results are in good agreement with available experimental results and confirm that the polarization of the solute by the continuum has important effects on the absolute and relative solvation energies. Frequency shifts and intensity variations in the infrared spectra due to the presence of the solvent are also presented. 0 1995 John Wiley & Sons, Inc.tomers may have important biological implications, such as mutagenesis. In addition, the effect of the environment on tautomeric equilibria may be dramatic, changing equilibrium constants several orders of magnitude. Recently, we reported gas-phase calculations on the tautomerism of uracil and cytosine molecules [9] using density functional theory (DFT); the results are in reasonable agreement with the avail-

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Nucleic acid bases studied by matrix isolation vibrational spectroscopy: Uracil and deuterated uracils

Cited by 122 publications

References 27 publications

FTIR and Raman Spectra Compared with Ab Initio Calculated Frequency Modes for 5-Aminouracil

FTIR and Raman Spectra Compared with Ab Initio Calculated Frequency Modes for 5-Aminouracil

Dissociative electron attachment to uracil deuterated at the N1 and N3 positions

Solvent effects in density functional calculations of uracil and cytosine tautomerism

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