Scaled quantum mechanical force fields and vibrational spectra of solid state nucleic acid constituents V: thymine and uracil

Florián, Jan; Hrouda, Vojtéch

doi:10.1016/0584-8539(93)80211-r

Cited by 60 publications

(79 citation statements)

References 37 publications

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“…Among these, the strong 727 cm −1 Raman band deserves mention, as it is assigned to the pyrimidine ring-stretching vibration commonly observed for all pyrimidines and derivatives at this wavenumber range. As in the case of Florian and Hrouda's work, [98] the wavenumbers predicted in this work show large deviations from observed ones in the high wavenumber region. This is as high as 80 cm −1 for one of the two carbonyl stretching bands and 47 cm −1 for the 1668 cm −1 C-C stretching band.…”

Section: Thyminesupporting

confidence: 49%

“…This is also observed in some bands by Aamouche et al [103] and Ghomi et al, [101] where both the Onsager model and the uracil dihydrate model were used. Also, the use of much higher basis sets in the present work as well as by Giese and McNaughton [100] have yielded better results as against those of Aamouche et al [103] The use of much smaller basis sets MINI-1, STO-3G, and the PM3 method by Florian and Hrouda [98] has reproduced accurately the IR and Raman wavenumbers reported by them in the solid state; this has been achieved through the consideration of a set of scale factors used for different types of force constants.…”

Section: Uracilmentioning

confidence: 47%

“…A wealth of information on the vibrational spectroscopic properties is available for uracil. The IR [98] and Raman [98 -100] spectra in the solid state and aqueous solution, [99,100] NIS spectra, [101] and SERS spectra [99,100] have all been reported. Raman spectroscopic studies of free uracil and modified uracil (2 -β-fluorodeoxyuridine) complexes with uracil-DNA glycosylase (UDG) repair enzyme have been reported.…”

Section: Uracilmentioning

confidence: 99%

“…The C 2 O band is not assigned in the solid-state Raman spectrum of polycrystalline thymine, [98] but is observed as a very strong peak at 1744 cm −1 in the solid-state IR spectrum. This band is accurately reproduced at 1742, 1741, and 1726 cm −1 by the MINI-1, STO-3G, and PM3 methods used in the study by Florian and Hrouda.…”

Section: Thyminementioning

confidence: 99%

“…This band is accurately reproduced at 1742, 1741, and 1726 cm −1 by the MINI-1, STO-3G, and PM3 methods used in the study by Florian and Hrouda. [98] The C 4 O Raman band is weak and appears at 1701 cm −1 , while it appears as a medium intensity shoulder at 1692 cm −1 in the IR spectrum; the MINI-1 basis set best reproduces these bands at 1699 cm −1 . The two strongest Raman bands occur in this spectrum at 1666 and 1363 cm −1 .…”

Section: Thyminementioning

confidence: 99%

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Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Shanmugasundaram¹,

Puranik²

2009

J Raman Spectroscopy

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Purines, pyrimidines, and the corresponding ribose monophosphates are ubiquitous biomolecules involved in several cellular processes-in DNA and RNA, signaling, and energy transactions. In the new and exciting field of DNA-inspired nanostructures, they are used as fundamental building blocks. Unique features of the nucleobases are that several tautomeric states are close in energy and the tautomeric equilibria are sensitive to exocyclic substitution and pH. Knowing the exact structure and tautomer(s) at physiological conditions is crucial to understand the substrate specificities and catalytic mechanisms of the many enzymes for which these nucleobases are substrates. Very few spectroscopic methods can distinguish between tautomers and provide solution structures. Vibrational spectroscopy has long been known to be an excellent tool to obtain reliable information on nucleic acids. However, even when good-quality spectra are available, isotope editing is required to make reliable band assignments and identify structures unequivocally. Density functional theoretical (DFT) methods have become indispensible in assisting the assignment of observed spectra to normal modes, identification of tautomers, and modeling of spectra of isotope-edited molecules. We review the performance of DFT methods in the prediction of nucleobases and their analogs. We find that even with modest basis sets, trends in vibrational spectra can be predicted adequately and guide assignments to normal modes of the molecule. Shifts in band positions induced upon isotope labeling are reproduced more reliably than the band positions. Scaling considerably improves the agreement between the computed and experimental spectra, but accurate prediction of vibrations of exocyclic groups like C O requires that solvent effects are taken into account.

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Section: Thyminesupporting

confidence: 49%

Section: Uracilmentioning

confidence: 47%

Section: Uracilmentioning

confidence: 99%

Section: Thyminementioning

confidence: 99%

Section: Thyminementioning

confidence: 99%

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Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Shanmugasundaram¹,

Puranik²

2009

J Raman Spectroscopy

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Vibrational analysis and spectra of orotic acid

et al. 2000

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Raman spectroscopic study of uridine nucleotides: structural information and conformational features

Carmona

Rodrı́guez-Casado

Molina

et al. 1999

J. Raman Spectrosc.

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Raman spectra of the sodium salts of uridine and deoxyuridine monophosphoric acid, Na 2 (3 -UMP)·4H 2 O, Na 2 (5-UMP)·7H 2 O and Na 2 (5 -dUMP)·5H 2 O, and the cadmium salt, [Cd(5 -UMP)(H 2 O) 2 ]·2H 2 O, were examined. Several spectral differences were observed owing to nucleoside conformational differences in the uridine residue. The spectroscopic characterization of the nucleoside structures was made on the basis of previous x-ray crystal studies of these compounds. Although the crystal structures of Ca(3 -UMP)·2H 2 O, Sr(3 -UMP)·4H 2 O and Ba(3 -UMP)·4H 2 O also reported here are as yet unknown, their nucleoside structures were inferred from the position of the phosphoester stretching band. These results enabled us to consider some novel Raman band markers as diagnostic of the C(3 )-endo and C(2 )-endo uridine conformations.

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Scaled quantum mechanical force fields and vibrational spectra of solid state nucleic acid constituents V: thymine and uracil

Cited by 60 publications

References 37 publications

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Vibrational analysis and spectra of orotic acid

Raman spectroscopic study of uridine nucleotides: structural information and conformational features

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