2D IRphoton echo of azido-probes for biomolecular dynamics

Abstract

The vibrations in the azido-, N3, asymmetric stretching region of 2′-azido-2′-deoxyuridine (N3dU) 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 N3dU 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 renders -N3 a very useful probe for 2D IR and other nonlinear IR studies: its signal is ca. 100 times that of nitrile.

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

“…7, 12 The presence of these two reporters within a close proximity in the same molecule results in significant vibrational coupling between their dipoles. As a result, the relative intensities of the infrared transitions are sufficiently different than expected from prior literature 7, 12, 28 as well as the calculated transition dipole ratio. The observed vibrational frequencies and relative intensities of the linear IR spectrum can often be predicted from the solutions to the Hamiltonian shown below: $$H=true(\begin{array}{cc}left{\epsilon }_{N_3}& left{\beta }_{12}\\ left{\beta }_{12}& left{\epsilon }_{CN}\end{array}true),$$ where β 12 represents the coupling between the azide (ε N 3 ) and nitrile (ε CN ) vibrational modes.…”

“…The observed change in relative intensities (10:1 vs. 2.7:1) clearly indicates the presence of coupling. 42 However, due to the large energy difference, 118 cm −1 , between the two uncoupled oscillators (2124 cm −1 for the azide group 12 and 2241.9 cm −1 for the nitrile group 7 ), the overall change in energy of the peaks is not expected to be significant. However, it is known that determining the coupling strength between these two transition dipoles through the splitting in the FTIR spectrum is sometimes difficult.…”

“…Specifically, the aliphatic azide substitutions are stable under most conditions and often avoid accidental Fermi resonances, allowing the azide reporter to more effectively detect local environment in peptides, proteins, and nucleosides. 2, 12, 25–27 Both the N 3 transition and the CN transition have many similar spectral properties and a direct comparison of these probes has been documented using 2’-azido-5-cyano-2’-deoxyuridine (N 3 CNdU). 10 The changes in vibrational frequency resulting from hydrogen bonding and sensitivity to local electric field changes of both localized infrared transitions offer many advantages to studies of structural dynamics.…”

2D attenuated total reflectance infrared spectroscopy reveals ultrafast vibrational dynamics of organic monolayers at metal-liquid interfaces

“…The azide group is a common vibrational probe in static and time-resolved infrared spectroscopy for the investigation of structural dynamics and environmental interactions. 38,40,[54][55][56][57] Formation of the monolayers results in a rather slow spectral diffusion for samples with two and 11 methylene groups between the azide group and the surface. Generally, an increase in length of the alkyl chain between the surface of immobilization and the vibrational probe also results in a smaller time-dependent inhomogeneity.…”

“…38,[54][55][56][57] In these studies, spectral diffusion of azide groups covalently attached to different alkyl backbones in bulk solution and different polar and apolar environments generally occurred with rather short time constants in a range of ≈0.5-2 ps. 38,54,55,57 This indicates a generally rapid loss of correlation for the azide vibrational probe. Comparing these values to the ML samples reported here, the spectral diffusion times are slower by at least a factor of 2-3 (Tables I and II).…”