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Development of Vibrational Frequency Maps for Nucleobases.

ABSTRACT: Vibrational spectroscopy provides a powerful tool to probe the structure and dynamics of nucleic acids because specific normal modes, particularly the base carbonyl stretch modes, are highly sensitive to the hydrogen bonding patterns and stacking configurations in these biomolecules. In this work, we develop vibrational frequency maps for the C?O and C?C stretches in nucleobases that allow the calculations of their site frequencies directly from molecular dynamics simulations. We assess the frequency maps by applying them to nucleobase derivatives in aqueous solutions and nucleosides in organic solvents and demonstrate that the predicted infrared spectra are in good agreement with experimental measurements. The frequency maps can be readily used to model the linear and nonlinear vibrational spectroscopy of nucleic acids and elucidate the molecular origin of the experimentally observed spectral features.

SUBMITTER: Jiang Y

PROVIDER: S-EPMC6820520 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Development of Vibrational Frequency Maps for Nucleobases.

Jiang Yaoyukun Y Wang Lu L

The journal of physical chemistry. B 20190701 27

Vibrational spectroscopy provides a powerful tool to probe the structure and dynamics of nucleic acids because specific normal modes, particularly the base carbonyl stretch modes, are highly sensitive to the hydrogen bonding patterns and stacking configurations in these biomolecules. In this work, we develop vibrational frequency maps for the C═O and C═C stretches in nucleobases that allow the calculations of their site frequencies directly from molecular dynamics simulations. We assess the freq ...[more]

PMID: 31260308

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Dataset Information

Development of Vibrational Frequency Maps for Nucleobases.

Publications

Development of Vibrational Frequency Maps for Nucleobases.

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