Integrated and dispersed photon echo studies of nitrile stretching vibration of 4-cyanophenol in methanol

Ultrafast Structure and Vibrational Dynamics of a Cyano-Containing Non-Fullerene Acceptor for Organic Solar Cells Revealed by Two-Dimensional Infrared Spectroscopy

Non-fullerene molecules, such as ITIC (3,9-bis(2-methylene-(3-(1,1-dicyanomethylene) indanone)-5,5,11,11-tetrakis(4-hexylphenyl)dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']-dithiophene), are among the most promising non-fullerene acceptors for organic solar cells (OSCs). In this work, using the cyano stretching mode as a vibrational marker, the structural and vibrational energy dynamics of ITIC were examined on an ultrafast time scale with two-dimensional infrared spectroscopy. Two IR-active modes studied here mainly correspond to two anti-symmetric combinations of symmetric and asymmetric stretching vibrations of two C≡N modes originating from two -C(CN)₂ chromophores that are located across the ITIC system, which were found to have significantly larger off-diagonal anharmonicity than their corresponding diagonal anharmonicities. This indicates strong anharmonic vibrational coupling between the two modes, which is supported by ab initio anharmonic frequency computations. Transient IR results indicate picosecond intramolecular vibrational energy transfer between the two C≡N modes upon excitation. The structural basis for these vibrational and energetic features is the conjugating molecular frame that is composed of a network of single/double bonds connecting the two -C(CN)₂ chromophores and may enable efficient vibration delocalization, in addition to its well-known electron delocalization capability. The importance of the results for the OSC applications is discussed.

Spectral line shapes in linear absorption and two-dimensional spectroscopy with skewed frequency distributions

The effect of Gaussian dynamics on the line shapes in linear absorption and two-dimensional correlation spectroscopy is well understood as the second-order cumulant expansion provides exact spectra. Gaussian solvent dynamics can be well analyzed using slope line analysis of two-dimensional correlation spectra as a function of the waiting time between pump and probe fields. Non-Gaussian effects are not as well understood, even though these effects are common in nature. The interpretation of the spectra, thus far, relies on complex case to case analysis. We investigate spectra resulting from two physical mechanisms for non-Gaussian dynamics, one relying on the anharmonicity of the bath and the other on non-linear couplings between bath coordinates. These results are compared with outcomes from a simpler log-normal dynamics model. We find that the skewed spectral line shapes in all cases can be analyzed in terms of the log-normal model, with a minimal number of free parameters. The effect of log-normal dynamics on the spectral line shapes is analyzed in terms of frequency correlation functions, maxline slope analysis, and anti-diagonal linewidths. A triangular line shape is a telltale signature of the skewness induced by log-normal dynamics. We find that maxline slope analysis, as for Gaussian dynamics, is a good measure of the solvent dynamics for log-normal dynamics.

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.

Selective incorporation of nitrile-based infrared probes into proteins via cysteine alkylation

The nitrile stretching vibration is increasingly used as a sensitive infrared probe of local protein environments. However, site-specific incorporation of a nitrile moiety into proteins is difficult. Here we show that various aromatic nitriles can be easily incorporated into peptides and proteins via either thiol alkylation or arylation reaction.

Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water

The bandwidth of the nitrile (C≡N) stretching vibration of 5-cyanotryptophan shows a significant broadening upon hydration. Thus, it has been proposed to be a useful infrared probe of the local hydration environment of proteins. However, the molecular mechanism underlying this hydration-induced spectral broadening is not known, making interpretation of the experimental results difficult. Herein, we investigate how interactions of water with various sites of 5-cyanoindole, the sidechain of 5-cyanotryptophan, affect its C≡N stretching vibration via a combined electronic structure/molecular dynamics approach. It is found that, besides those interactions with the nitrile group, interactions of water with the indole ring also play a significant role in mediating the C≡N stretching frequency. Thus, this study provides a molecular basis for understanding how hydration affects the C≡N stretching band of 5-cyanotryptophan. In addition, an empirical model, which includes interactions of water with both the nitrile and indole groups, is developed for predicting the C≡N stretching vibrational band via molecular dynamics simulations.

The Two Dimensional Vibrational Echo of a Nitrile Probe of the Villin HP35 Protein

2D IR spectroscopy was used to probe the hydrophobic core structure of the 35-residue Villin headpiece subdomain, HP35, by monitoring the C≡N vibrational stretching band of a cyano substituted phenylalanine (Phe). The presence of two humps in the vibrational frequency distribution in the folded equilibrium state is revealed. They represent two states that exchange more slowly than ca. 10 ps. The two CN stretch mode peak frequencies (and their equilibrium populations) are 2228.7 (44%) and 2234.5 cm(-1) (56%). The two CN modes have different frequency-frequency correlation times of 7.4 ps and 1.6 ps respectively. These results suggest that the population with the higher frequency CN group is partly exposed whereas the other CN mode experiences a hydrophobic like environment.

5-Cyanotryptophan as an Infrared Probe of Local Hydration Status of Proteins

The nitrile (C≡N) stretching vibration is sensitive to environment, making nitrile-derivatized amino acids an increasingly utilized tool to study various biological processes. Herein, we show that the bandwidth of the C≡N stretching vibration of 5-cyanotryptophan is particularly sensitive to water, rendering it an attractive infrared probe of local hydration status. We confirm the utility of this probe in biological applications by using it to examine how the hydration status of individual tryptophan sidechains of an antimicrobial peptide, indolicidin, changes upon peptide binding to model membranes. Furthermore, we show that p-cyanophenylalanine and 5-cyanotryptophan constitute a useful fluorescence energy transfer pair.