Anharmonic Vibrational Modes of Nucleic Acid Bases Revealed by 2D IR Spectroscopy
Name
Tokmakoff_Anharmonic vibrational.pdf
Size
1.73 MB
Format
Adobe PDF
Checksum (MD5)
b7a9a20d97015288f724df83358c2c47
Author(s)
Peng, Chunte
Jones, Kevin C.
Tokmakoff, Andrei
Date Issued
August 2011
Journal
Journal of the American Chemical Society
Publisher
American Chemical Society (ACS)
Citation
Peng, Chunte Sam, Kevin C. Jones, and Andrei Tokmakoff. “Anharmonic Vibrational Modes of Nucleic Acid Bases Revealed by 2D IR Spectroscopy.” Journal of the American Chemical Society 133.39 (2011): 15650–15660. © 2011 American Chemical Society
Version
Author's final manuscript
Abstract
Polarization-dependent two-dimensional infrared (2D IR) spectra of the purine and pyrimadine base vibrations of five nucleotide monophosphates (NMPs) were acquired in D[subscript 2]O at neutral pH in the frequency range 1500–1700 cm[superscript –1]. The distinctive cross-peaks between the ring deformations and carbonyl stretches of NMPs indicate that these vibrational modes are highly coupled, in contrast with the traditional peak assignment, which is based on a simple local mode picture such as C═O, C═N, and C═C double bond stretches. A model of multiple anharmonically coupled oscillators was employed to characterize the transition energies, vibrational anharmonicities and couplings, and transition dipole strengths and orientations. No simple or intuitive structural correlations are found to readily assign the spectral features, except in the case of guanine and cytosine, which contain a single local CO stretching mode. To help interpret the nature of these vibrational modes, we performed density functional theory (DFT) calculations and found that multiple ring vibrations are coupled and delocalized over the purine and pyrimidine rings. Generally, there is close correspondence between the experimental and computational results, provided that the DFT calculations include explicit waters solvating hydrogen-bonding sites. These results provide direct experimental evidence of the delocalized nature of the nucleotide base vibrations via a nonperturbative fashion and will serve as building blocks for constructing a structure-based model of DNA and RNA vibrational spectroscopy.
MIT Department
Massachusetts Institute of Technology. Department of Chemistry
Terms of Use
Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1021/ja205636h
