2D IR photon echo of azido-probes for biomolecular dynamics

Phys Chem Chem Phys. 2011 Feb 14;13(6):2237-41. doi: 10.1039/c0cp01625j. Epub 2010 Dec 2.

Abstract

The vibrations in the azido-, N(3), asymmetric stretching region of 2'-azido-2'-deoxyuridine (N(3)dU) are examined by two-dimensional infrared spectroscopy. In water and tetrahydrofuran (THF), the spectra display a single sharp diagonal peak that shows solvent sensitivity. The frequency-frequency correlation time in water is 1.5 ps, consistent with H-bond making and breaking dynamics. The 2D IR spectrum is reproduced for N(3)dU in water based on a model correlation function and known linear response functions. Its large extinction coefficient, vibrational frequency outside the protein and nucleic acid IR absorption, and sensitivity to water dynamics render -N(3) a very useful probe for 2D IR and other nonlinear IR studies: its signal is ca. 100 times that of nitriles.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Azides / chemistry*
  • Deoxyuridine / analogs & derivatives*
  • Deoxyuridine / chemistry
  • Furans / chemistry*
  • Hydrogen Bonding
  • Molecular Dynamics Simulation
  • Nitriles / chemistry*
  • Spectrophotometry, Infrared
  • Water / chemistry*

Substances

  • Azides
  • Furans
  • Nitriles
  • Water
  • 2'-azido-2'-deoxyuridine
  • tetrahydrofuran
  • Deoxyuridine