ArticleThe journal of physical chemistry. B2019
Development of Vibrational Frequency Maps for Nucleobases.
Article in The journal of physical chemistry. B, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- NAIRDB: a database of Fourier transform infrared (FTIR) data for nucleic acids.Nucleic acids research · 2025Article
- Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes.Journal of chemical theory and computation · 2024Article
- Unraveling the Structure-Spectrum Relationship of Yeast Phenylalanine Transfer RNA: Insights from Theoretical Modeling of Infrared Spectroscopy.Biochemistry · 2024Article
- Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy.International journal of molecular sciences · 2024Article
- Investigating the Spectroscopy of the Gas Phase Guanine-Cytosine Pair: Keto versus Enol Configurations.The journal of physical chemistry letters · 2023Article
- Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation.Computers in biology and medicine · 2023Article
- Modeling the Infrared Spectroscopy of Oligonucleotides withThe journal of physical chemistry. B · 2023Article
- Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.Chemical reviews · 2020Review
- Modeling the vibrational couplings of nucleobases.The Journal of chemical physics · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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.
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