Two-Dimensional Infrared Study of Vibrational Coupling between Azide and Nitrile Reporters in a RNA Nucleoside

The vibrations in the azide, N3, asymmetric stretching region and nitrile, CN, symmetric stretching region of 2′-azido-5-cyano-2′-deoxyuridine (N3CNdU) are examined by two-dimensional infrared (2D IR) spectroscopy. At earlier waiting times, the 2D IR spectrum shows the presence of both vibrational t...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2016-09, Vol.120 (35), p.9387-9394
Main Authors: Schmitz, Andrew J, Hogle, David G, Gai, Xin Sonia, Fenlon, Edward E, Brewer, Scott H, Tucker, Matthew J
Format: Article
Language:English
Subjects:
Azides - chemistry
Coupling
Dynamical systems
Infrared spectroscopy
Nitriles
Nitriles - chemistry
Nucleosides
Quantum Theory
Ribonucleic acids
RNA - chemistry
Spectrophotometry, Infrared
Stretching
Vibration
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Summary:The vibrations in the azide, N3, asymmetric stretching region and nitrile, CN, symmetric stretching region of 2′-azido-5-cyano-2′-deoxyuridine (N3CNdU) are examined by two-dimensional infrared (2D IR) spectroscopy. At earlier waiting times, the 2D IR spectrum shows the presence of both vibrational transitions along the diagonal and off-diagonal cross peaks indicating vibrational coupling. The coupling strength is determined from the off-diagonal anharmonicity to be 66 cm–1 for the intramolecular distance of ∼7.9 Å, based on a structural map generated for this model system. In addition, the frequency–frequency correlation decay is detected, monitoring the solvent dynamics around each individual probe position. Overall, these vibrational reporters can be utilized in tandem to simultaneously track global structural information and fast structural fluctuations.
ISSN:1520-6106
1520-5207
DOI:10.1021/acs.jpcb.6b07212