Vibrational chromophores that are sensitive to local electrostatic environment are useful probes of structural variations of proteins on subnanosecond time scales, but their short vibrational lifetimes often limit their applicability. Here we explore a possibility to increase the lifetime of nitrile probes by introducing heavy atoms between the probe and protein side chains. Stereoisomers of thiocyanato-and selenocyanato-derivatized prolines, Pro-SCN and Pro-SeCN, are synthesized, and their CN stretch lifetimes in D 2 O and chloroform are measured with polarization-controlled IR pump−probe spectroscopy. The measured lifetimes of 170−330 ps for Pro-SeCN are three to four times longer than those for Pro-SCN, indicating that selenium atom is more effective than sulfur atom in blocking the intramolecular vibrational relaxation pathways of the CN stretch mode. This is further confirmed by carrying out nonequilibrium molecular dynamics simulations of the vibrational relaxation processes. Given the crucial role of the proline residue in determining protein structures, we anticipate that the Pro-SeCN probe can be an excellent site-specific probe of changes in protein local environment.

The infrared (IR) probe often suffers from an unexpected complex absorption profile due to the Fermi resonance and short vibrational lifetime, which restricts the application of time-resolved IR spectroscopy to investigate the site-specific structural dynamics of the protein. Researchers have found that isotope substitution to the IR probe not only removes the Fermi resonance but also extends the dynamic observation window with a prolonged vibrational lifetime. This method has been successfully applied to modify the vibrational properties of many IR probes for time-resolved spectroscopy and imaging. In this study, the effect of isotope substitution (15N) on the vibrational properties of the azide stretching band in 4-azido-L-phenylalanine has been investigated using ultrafast pump-probe and 2D-IR spectroscopy. In contrast to the earlier reports, it has been observed that the Fermi resonance remains unchanged even after isotope substitution, and there is very little change in the vibrational relaxation dynamics as well. Anharmonic frequency analysis reveals that the α-N atom of N3 is being shared between the two transitions participating in the Fermi resonance and gets affected similarly due to isotope labeling. Hence, this study unveils the specific circumstance at which the isotope labeling strategy may not be successful in eliminating the Fermi resonance band and explains the molecular origin behind it. This study also suggests definitive approaches on how to overcome the limitations related to the Fermi resonance to extend the development and application of this IR probe for biological research.

Azido stretch mode in a variety of azido-derivatized nonnatural amino acids and nucleotides have been used as a site-specific infrared (IR) probe for monitoring changes in their conformations and local...