Vibrational motions of bases of nucleic acids as revealed by neutron inelastic scattering and resonance Raman spectroscopy. 1. Adenine and its deuterated species

Dhaouadi, Zoubeida; Ghomi, Mahmoud; Austin, J. C.; Girling, Reuben B.; Hester, R. E.; Mojzeš, Peter; Chinsky, L.; Turpin, Pierre‐Yves; Coulombeau, C.; Jobic, H.; Tomkinson, J.

doi:10.1021/j100107a016

Cited by 80 publications

(88 citation statements)

References 11 publications

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“…The INS spectrum recorded for adenine is represented in Fig. 5, and constitutes a significant improvement relative to the previously reported one, 3 which was acquired in 1992 at the previous version of the TOSCA spectrometer (TFXA) at ISIS (UK) 48 with a far lower resolution and signal-to-noise ratio.…”

Section: Vibrational Analysismentioning

confidence: 91%

“…[3][4][5][6][7][8][9] Fourteen different tautomeric species were found, both for the gas-phase and the aqueous solution, 10 comprising four amino and ten imino forms. In fact, adenine's tautomeric equilibrium has been studied in great detail and at different theoretical levels.…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, the INS data presently reported were obtained using the TOSCA spectrometer of the ISIS pulsed neutron and muon source (United Kingdom), which represent a substantial improvement relative to the previously reported results that were acquired in the former TFXA configuration of this spectrometer. 3 …”

mentioning

confidence: 99%

“…3(A) and 5(A)), which also have contributions from C-N stretching modes (Table 1) in agreement with earlier studies. 3,46 In the high frequency spectral range, five bands are expected to occur due to the N-H/C-H stretching vibrations (including the n s (NH 2 ) and n a (NH 2 ), …”

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confidence: 99%

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Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study

et al. 2013

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A full conformational study of solid-state anhydrous adenine is reported, using vibrational spectroscopy techniques coupled to DFT calculations, for the isolated molecule and the solid. In both cases, the N9H-amino tautomer was found to be the predominant species, followed by the N7H-amino form. An excellent agreement was achieved between experiment and theory, both for wavenumbers and intensities (without the need for scaling). A complete spectral assignment was performed, since all vibrational spectroscopic techniques were available to this study -FTIR, Raman and INS -allowing us to detect and interpret even the lowest frequency vibrational bands, not previously accessed. The quantum mechanical calculations presently carried out represent the highest theoretical level applied so far to the study of nucleobases.

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Section: Vibrational Analysismentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study

et al. 2013

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“…The detailed results of harmonic and anharmonic frequency DFT calculations for the isolated nucleobases are reported in the supplementary material (Tables 1-5) where they are compared with the available experimental data. Assignments of vibrational modes were performed by visual inspection of the atomic displacements along normal modes and by comparison with the assignments reported in the literature 31,32,[34][35][36]39,[144][145][146][147] .…”

Section: Monomersmentioning

confidence: 99%

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Fornaro

Biczysko

Monti

et al. 2014

Phys. Chem. Chem. Phys.

100

113

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Computational spectroscopy techniques have become in the last years effective means to analyze and assign infrared (IR) spectra for molecular systems of increasing dimensions and in different environments. However, transition from compilations of harmonic data to full anharmonic simulations of spectra is still under way. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed to a quantitative reproduction of the spectra of nucleic acid bases complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work, we have chosen two popular and inexpensive approaches to model dispersion interaction, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.

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Vibrational spectra of nucleic acid bases and their Watson-Crick pair complexes

et al. 1999

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Vibrational motions of bases of nucleic acids as revealed by neutron inelastic scattering and resonance Raman spectroscopy. 1. Adenine and its deuterated species

Cited by 80 publications

References 11 publications

Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study

Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Vibrational spectra of nucleic acid bases and their Watson-Crick pair complexes

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