Dephasing Dynamics across Different Local Vibrational Modes and Crystalline Environments

The perturbed free induction decay (PFID) observed in ultrafast infrared spectroscopy was used to unveil the rates at which different vibrational modes of the same atomic-scale defect can interact with their environment. The N_{3}VH^{0} defect in diamond provided a model system, allowing a comparison of stretch and bend vibrational modes within different crystal lattice environments. The observed bend mode (first overtone) exhibited dephasing times T_{2}=2.8(1)  ps, while the fundamental stretch mode had surprisingly faster dynamics T_{2}<1.7  ps driven by its more direct perturbation of the crystal lattice, with increased phonon coupling. Further, at high defect concentrations the stretch mode's dephasing rate was enhanced. The ability to reliably measure T_{2} via PFID provides vital insights into how vibrational systems interact with their local environment.

Cyano-tryptophans as dual infrared and fluorescence spectroscopic labels to assess structural dynamics in proteins

By moving the cyano group position on the indole ring, both artificial amino acids report differently to their microscopic environment.

C≡N stretching vibration of 5-cyanotryptophan as an infrared probe of protein local environment: what determines its frequency?

Recently it has been suggested that the C≡N stretching vibration of a tryptophan analog, 5-cyanotryptophan, could be used as an infrared probe of the local environment, especially the hydration status, of tryptophan residues in proteins. However, the factors that influence the frequency of this vibrational mode are not understood. To determine these factors, herein we carried out linear and nonlinear infrared measurements on the C≡N stretching vibration of the sidechain of 5-cyanotryptophan, 3-methyl-5-cyanoindole, in a series of protic and aprotic solvents. We found that while the C≡N stretching frequencies obtained in these solvents do not correlate well with any individual Kamlet-Taft solvent parameter, i.e., π* (polarizability), β (hydrogen bond accepting ability), and α (hydrogen bond donating ability), they do however, collapse on a straight line when plotted against σ = π* + β - α. This linear relationship provides a firm indication that both specific interactions, i.e., hydrogen-bonding interactions with the C≡N (through α) and indole N-H (through β) groups, and non-specific interactions with the molecule (through π*) work together to determine the C≡N stretching frequency, thus laying a quantitative framework for applying 5-cyanotryptophan to investigate the microscopic environment of proteins in a site-specific manner. Furthermore, two-dimensional and pump-probe infrared measurements revealed that a significant portion (∼31%) of the ground state bleach signal has a decay time constant of ∼12.3 ps, due to an additional vibrational relaxation channel, making it possible to use 5-cyanotryptophan to probe dynamics occurring on a timescale on the order of tens of picoseconds.