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

Santamaría, Rubén; Charro, E.; Zacarias, Angelica; Castro, Miguel

doi:10.1002/(sici)1096-987x(19990415)20:5<511::aid-jcc4>3.0.co;2-8

Cited by 123 publications

(117 citation statements)

References 66 publications

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“…Moreover, at 1526 and 1583 cm 1 lines appeared both in the Raman Table 2. Raman lines and their assignments of the solid state of eritadenine based on this study, and the work of Santamaria et al 15 spectrum of MAIR and the Raman spectrum of eritadenine. These vibrations are assigned to the deformation of R5, R6 and the stretching of N9-C5 0 , N9-C4 0 respectively, since this region is the only common feature of the two compounds.…”

Section: Resultssupporting

confidence: 63%

“…2(D)) were recorded, and Raman lines that significantly changed throughout the synthesis process are listed in Table 1. The assignments of the Raman lines of adenine are according to the study of Santamaria et al 15 and of D-ribose, according to Carmona and Molina. 16 The Raman spectrum of eritadenine was established by comparing the spectra of all compounds involved and by investigating how new bonds and breaking of existing bonds, i.e.…”

Section: Resultsmentioning

confidence: 99%

“…Raman lines and their assignments for the solid states of adenine (Santamaria et al15 ), ribose (Carmona and Molina 16 ), MAIR, and eritadenine (from this study)…”

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confidence: 99%

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Raman analysis of synthetic eritadenine

Enman

Ramser

Berglund

2008

J Raman Spectroscopy

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Eritadenine, 2(R),3(R)-dihydroxy-4-(9-adenyl)-butyric acid, is a cholesterol-reducing compound naturally occurring in the shitake mushroom (Lentinus edodes). To identify the unknown Raman spectrum of this compound, pure synthetic eritadenine was examined and the vibrational modes were assigned by following the synthesis pathway. This was accomplished by comparing the known spectra of the starting compounds adenine and D-ribose with the spectra of a synthesis intermediate, methyl 5-(6-Aminopurin-9H-9-yl)-2,3-O-isopropylidene-5-deoxy-b-D-ribofuranoside (MAIR) and eritadenine. In the Raman spectrum of eritadenine, a distinctive vibrational mode at 773 cm −1 was detected and ascribed to vibrations in the carbon chain, n(C-C). A Raman line that arose at 1212 cm −1 , both in the Raman spectrum of MAIR and eritadenine, was also assigned to n(C-C). Additional Raman lines detected at 1526 and at 1583 cm −1 in the Raman spectrum of MAIR and eritadenine were assigned to n(N-C) and a deformation of the purine ring structure. In these cases the vibrational modes are due to the linkage between adenine and the ribofuranoside moiety for MAIR, and between adenine and the carbon chain for eritadenine. This link is also the cause for the disappearance of adenine specific Raman lines in the spectrum of both MAIR and eritadenine. Several vibrations observed in the spectrum of D-ribose were not observed in the Raman spectrum of eritadenine due to the absence of the ribose ring structure. In the Raman spectrum of MAIR some of the D-ribose specific Raman lines disappeared due to the introduction of methyl and isopropylidene moieties to the ribose unit. With the approach presented in this study the so far unknown Raman spectrum of eritadenine could be successfully identified and is presented here for the first time.

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Section: Resultssupporting

confidence: 63%

Section: Resultsmentioning

confidence: 99%

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Raman analysis of synthetic eritadenine

Enman

Ramser

Berglund

2008

J Raman Spectroscopy

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“…Furthermore, all the experimental peaks could be unambiguously assigned to normal vibrational modes without the need for scaling. It is noteworthy that the present vibrational analysis differs from earlier reported studies 5,14,45 (especially in the low wavenumber region), since these considered a planar (C s ) calculated conformation for adenine which is a saddle point. A very good quality experimental Raman spectrum was obtained for adenine (Fig.…”

Section: Vibrational Analysismentioning

confidence: 60%

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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“…We would expect the lowest in-plane vibrational frequencies to be of the order of a few hundred wave numbers. By comparison with matrix isolation spectra and calculations, the first in-plane vibration in the ground state would be expected at about 340 cm À1 [22][23][24]. We have performed calculations at the MP2/6G 311 level, obtaining similar results.…”

Section: Discussionmentioning

confidence: 78%

REMPI spectroscopy of cytosine

Nir

Müller

Grace

et al. 2002

Chemical Physics Letters

165

229

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We report resonant two-photon ionization spectra of laser desorbed, jet cooled, cytosine, 1-methyl cytosine, 5-methyl cytosine, and dimers of these. Unlike other pyrimidine bases, cytosine exhibits vibronic spectra with sharp features in two spectral regions, separated by about 5000 cm À1 . We interpret these as being due to two tautomeric forms, one keto and one enol. The dimers absorb at wavelengths that are intermediate between those of the two monomer forms. By UV-UV hole burning we determined the numbers of isomers contributing to each spectrum and by delayed two color ionization we determined triplet lifetimes. We observed hydrogen transfer between bases both in collisions between monomers and after photo-excitation in clusters. Ó

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

Cited by 123 publications

References 66 publications

Raman analysis of synthetic eritadenine

Raman analysis of synthetic eritadenine

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

REMPI spectroscopy of cytosine

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